I am trying to do ttest for each plate which has equal number of disease and controls. by searching this forum I found one posting suggesting OP to use "by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))". when i modified this for my use I used to get the pvalues for each plate, recently upgraded to R2.9.x and now i am getting following error when i use this> by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))Error in t.test.formula(IL1Ra ~ Group, data = .sub) : grouping factor must have exactly 2 levels I checked my data file and the plate ID has "P16-P47" and the disease column is "Y/N". I have search all but could not locate the answer. Can anyone suggest me the direction where i am going wrong. for more detail i amm posting a part of my data. SampleID PlateID Sex Disease Duration Age prt1 prt2 prt3 prt4 1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43 2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36 3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52 4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04 5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36 6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75 7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69 8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61 9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72 10 P16 M N 0.916030215 242.3011559 36.40117263 90.1 35962.08 11 P16 F Y 14975.25 42.08281552 133.8052501 29.0570764 260.55 1280.29 12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6 13 P16 F Y 2922 25.08300169 231.6043765 9.022844487 902.53 37571.39 14 P16 F Y 12053.25 37.49924765 158.6370595 24.90606549 1.63 471.15 15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49 16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21 17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27 18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89 19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15 20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86 21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47 22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12 23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78 24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62 25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14 26 P17 M Y 12053.25 50.91548265 173.7764722 18.90280088 52.25 15962.05 27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95 28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39 29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48 30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83 31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02 32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84 33 P17 M Y 8766 31.74913978 220.2561296 34.40329218 130.31 2377.36 34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 19587.61 35 P17 M Y 12053.25 36.1661567 212.1613578 96.51775947 621.42 3269.9 36 P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27 37 P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77 38 P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32 248857.58 39 P18 F N 14.2496731 538.5430144 54.34303351 396 4432.94 40 P18 M N 11.83263428 236.8218238 48.37595532 148.94 1414.11 41 P18 M N 7.582851659 322.2342976 87.83185053 280.84 16294.98 42 P18 F N 8.83266713 288.4507237 30.47472075 256.38 348.03 43 P18 M N 43.58245741 297.1312253 3.276042927 368.22 3627.89 44 P18 F N 45.49916004 297.1312253 160.4104035 635.12 1325.33 45 P18 M N 10.83264523 179.2726374 39.85155791 64.24 763.59 46 P18 M N 18.5827312 3389.23762 71.66394523 1105.37 45291.49 47 P18 F N 7.416300711 1345.377837 29.62228101 1195.82 19241.32 48 P18 M Y 4383 19.16634287 137.1490061 20.22826506 157.45 4026.95 49 P18 M Y 4748.25 19.0830674 226.7358839 93.61453199 507.45 1274.6 50 P18 M Y 4748.25 19.0830674 285.870034 60.87840486 330.91 586.98 51 P18 M Y 3652.5 12.33297048 195.6870101 39.56741133 48.1 16561.4 52 P18 F Y 4017.75 11.24970596 145.4550742 42.55095042 20.56 732.42 53 P18 F Y 1461 3.999956195 385.813107 63.1515775 204.62 2347.46 54 P18 M Y 4748.25 16.08310025 117.965944 58.03693906 78.33 2709.32 55 P18 M Y 1826.25 13.99984668 175.9106574 67.41377621 65.53 2069.11 56 P18 M Y 730.5 14.9158769 89.68575957 27.91740153 22.62 389.59 57 P18 F Y 6209.25 17.4161912 191.9295031 32.60582011 127.63 20291.34 58 P18 F Y 365.25 5.249771666 121.723451 61.7308446 49.39 11463.27 59 P18 F Y 4748.25 18.33290477 179.0748739 53.20644719 46.16 111361.43 60 P18 M Y 1826.25 6.083209766 330.6801911 27.06496179 489.04 12258.96 61 P18 F Y 3287.25 17.58274215 182.8323809 29.48020772 115.1 15324.67 62 P18 F Y 3652.5 44.16606909 248.4898719 87.24178099 139.33 16443.86 63 P19 M N 37.99958385 2197.263844 86.43305867 1492.06 3547.88 64 P19 F N 37.58252312 4588.403833 152.9115464 1722.46 9243.22 65 P19 F N 34.91565787 316.0623502 17.19804354 1582.79 12217.62 66 P19 F N 42.74901931 213.1054131 32.99689553 212.94 2714.66 67 P19 F N 10.08316596 4715.658374 50.91906722 1543.61 2490.68 68 P19 F N 43.33263099 2.258320699 0.524578302 561.12 5985.07 69 P19 F Y 365.25 8.999901438 208.5132426 32.8293986 45.72 2051.68 70 P19 M Y 4748.25 12.83262333 0 0 192.51 1255.58 71 P19 M Y 1461 16.83257952 218.2716049 65.82629413 255.01 4486.39 72 P19 M Y 5844 17.4161912 102.60631 27.80449065 49.77 622.01 73 P19 M Y 4748.25 18.33290477 182.9692941 9.965221488 159.66 2392.13 74 P19 F Y 730.5 17.24964025 100.8842461 27.97198758 157.25 176209.9 75 P19 M Y 4383 16.41620215 0.098187856 0 171.67 65286.23 76 P19 M Y 1461 6.16648524 962.1232959 112.1204345 81.67 870.82 -- View this message in context: http://www.nabble.com/need-help-for-t.test-using-%22by%22-tp25035006p25035006.html Sent from the R help mailing list archive at Nabble.com.
any one 1Rnwb wrote:> > I am trying to do ttest for each plate which has equal number of disease > and controls. by searching this forum I found one posting suggesting OP to > use "by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))". when i > modified this for my use I used to get the pvalues for each plate, > recently upgraded to R2.9.x and now i am getting following error when i > use this > > by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)) > Error in t.test.formula(IL1Ra ~ Group, data = .sub) : > grouping factor must have exactly 2 levels > > I checked my data file and the plate ID has "P16-P47" and the disease > column is "Y/N". I have search all but could not locate the answer. Can > anyone suggest me the direction where i am going wrong. > for more detail i amm posting a part of my data. > > SampleID PlateID Sex Disease Duration Age prt1 prt2 prt3 prt4 > 1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43 > 2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36 > 3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52 > 4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04 > 5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36 > 6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75 > 7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69 > 8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61 > 9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72 > 10 P16 M N 0.916030215 242.3011559 36.40117263 90.1 35962.08 > 11 P16 F Y 14975.25 42.08281552 133.8052501 29.0570764 260.55 1280.29 > 12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6 > 13 P16 F Y 2922 25.08300169 231.6043765 9.022844487 902.53 37571.39 > 14 P16 F Y 12053.25 37.49924765 158.6370595 24.90606549 1.63 471.15 > 15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49 > 16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21 > 17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27 > 18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89 > 19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15 > 20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86 > 21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47 > 22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12 > 23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78 > 24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62 > 25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14 > 26 P17 M Y 12053.25 50.91548265 173.7764722 18.90280088 52.25 15962.05 > 27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95 > 28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39 > 29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48 > 30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83 > 31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02 > 32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84 > 33 P17 M Y 8766 31.74913978 220.2561296 34.40329218 130.31 2377.36 > 34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 19587.61 > 35 P17 M Y 12053.25 36.1661567 212.1613578 96.51775947 621.42 3269.9 > 36 P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27 > 37 P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77 > 38 P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32 248857.58 > 39 P18 F N 14.2496731 538.5430144 54.34303351 396 4432.94 > 40 P18 M N 11.83263428 236.8218238 48.37595532 148.94 1414.11 > 41 P18 M N 7.582851659 322.2342976 87.83185053 280.84 16294.98 > 42 P18 F N 8.83266713 288.4507237 30.47472075 256.38 348.03 > 43 P18 M N 43.58245741 297.1312253 3.276042927 368.22 3627.89 > 44 P18 F N 45.49916004 297.1312253 160.4104035 635.12 1325.33 > 45 P18 M N 10.83264523 179.2726374 39.85155791 64.24 763.59 > 46 P18 M N 18.5827312 3389.23762 71.66394523 1105.37 45291.49 > 47 P18 F N 7.416300711 1345.377837 29.62228101 1195.82 19241.32 > 48 P18 M Y 4383 19.16634287 137.1490061 20.22826506 157.45 4026.95 > 49 P18 M Y 4748.25 19.0830674 226.7358839 93.61453199 507.45 1274.6 > 50 P18 M Y 4748.25 19.0830674 285.870034 60.87840486 330.91 586.98 > 51 P18 M Y 3652.5 12.33297048 195.6870101 39.56741133 48.1 16561.4 > 52 P18 F Y 4017.75 11.24970596 145.4550742 42.55095042 20.56 732.42 > 53 P18 F Y 1461 3.999956195 385.813107 63.1515775 204.62 2347.46 > 54 P18 M Y 4748.25 16.08310025 117.965944 58.03693906 78.33 2709.32 > 55 P18 M Y 1826.25 13.99984668 175.9106574 67.41377621 65.53 2069.11 > 56 P18 M Y 730.5 14.9158769 89.68575957 27.91740153 22.62 389.59 > 57 P18 F Y 6209.25 17.4161912 191.9295031 32.60582011 127.63 20291.34 > 58 P18 F Y 365.25 5.249771666 121.723451 61.7308446 49.39 11463.27 > 59 P18 F Y 4748.25 18.33290477 179.0748739 53.20644719 46.16 111361.43 > 60 P18 M Y 1826.25 6.083209766 330.6801911 27.06496179 489.04 12258.96 > 61 P18 F Y 3287.25 17.58274215 182.8323809 29.48020772 115.1 15324.67 > 62 P18 F Y 3652.5 44.16606909 248.4898719 87.24178099 139.33 16443.86 > 63 P19 M N 37.99958385 2197.263844 86.43305867 1492.06 3547.88 > 64 P19 F N 37.58252312 4588.403833 152.9115464 1722.46 9243.22 > 65 P19 F N 34.91565787 316.0623502 17.19804354 1582.79 12217.62 > 66 P19 F N 42.74901931 213.1054131 32.99689553 212.94 2714.66 > 67 P19 F N 10.08316596 4715.658374 50.91906722 1543.61 2490.68 > 68 P19 F N 43.33263099 2.258320699 0.524578302 561.12 5985.07 > 69 P19 F Y 365.25 8.999901438 208.5132426 32.8293986 45.72 2051.68 > 70 P19 M Y 4748.25 12.83262333 0 0 192.51 1255.58 > 71 P19 M Y 1461 16.83257952 218.2716049 65.82629413 255.01 4486.39 > 72 P19 M Y 5844 17.4161912 102.60631 27.80449065 49.77 622.01 > 73 P19 M Y 4748.25 18.33290477 182.9692941 9.965221488 159.66 2392.13 > 74 P19 F Y 730.5 17.24964025 100.8842461 27.97198758 157.25 176209.9 > 75 P19 M Y 4383 16.41620215 0.098187856 0 171.67 65286.23 > 76 P19 M Y 1461 6.16648524 962.1232959 112.1204345 81.67 870.82 > > > >-- View this message in context: http://www.nabble.com/need-help-for-t.test-using-%22by%22-tp25035006p25043601.html Sent from the R help mailing list archive at Nabble.com.
On Aug 19, 2009, at 9:00 AM, 1Rnwb wrote:> > any oneI looked at your posting yesterday and could not figure out what your statistical question was, nor could I figure out how the t.test formula related to the column names in the data.frame. I saw no Group or IL1Ra variables in your data. I also tried to import that data and found that you had more column headers than columns. I gave up. -- DW> > 1Rnwb wrote: >> >> I am trying to do ttest for each plate which has equal number of >> disease >> and controls. by searching this forum I found one posting >> suggesting OP to >> use "by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))". >> when i >> modified this for my use I used to get the pvalues for each plate, >> recently upgraded to R2.9.x and now i am getting following error >> when i >> use this >>> by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)) >> Error in t.test.formula(IL1Ra ~ Group, data = .sub) : >> grouping factor must have exactly 2 levels >> >> I checked my data file and the plate ID has "P16-P47" and the disease >> column is "Y/N". I have search all but could not locate the answer. >> Can >> anyone suggest me the direction where i am going wrong. >> for more detail i amm posting a part of my data. >> >> SampleID PlateID Sex Disease Duration Age prt1 prt2 prt3 prt4 >> 1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43 >> 2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36 >> 3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52 >> 4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04 >> 5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36 >> 6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75 >> 7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69 >> 8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61 >> 9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72 >> 10 P16 M N 0.916030215 242.3011559 36.40117263 90.1 35962.08 >> 11 P16 F Y 14975.25 42.08281552 133.8052501 29.0570764 260.55 1280.29 >> 12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6 >> 13 P16 F Y 2922 25.08300169 231.6043765 9.022844487 902.53 37571.39 >> 14 P16 F Y 12053.25 37.49924765 158.6370595 24.90606549 1.63 471.15 >> 15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49 >> 16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 >> 41823.21 >> 17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27 >> 18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89 >> 19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15 >> 20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86 >> 21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47 >> 22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12 >> 23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78 >> 24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62 >> 25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14 >> 26 P17 M Y 12053.25 50.91548265 173.7764722 18.90280088 52.25 >> 15962.05 >> 27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95 >> 28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39 >> 29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48 >> 30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83 >> 31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02 >> 32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84 >> 33 P17 M Y 8766 31.74913978 220.2561296 34.40329218 130.31 2377.36 >> 34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 >> 19587.61 >> 35 P17 M Y 12053.25 36.1661567 212.1613578 96.51775947 621.42 3269.9 >> 36 P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27 >> 37 P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77 >> 38 P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32 >> 248857.58 >> 39 P18 F N 14.2496731 538.5430144 54.34303351 396 4432.94 >> 40 P18 M N 11.83263428 236.8218238 48.37595532 148.94 1414.11 >> 41 P18 M N 7.582851659 322.2342976 87.83185053 280.84 16294.98 >> 42 P18 F N 8.83266713 288.4507237 30.47472075 256.38 348.03 >> 43 P18 M N 43.58245741 297.1312253 3.276042927 368.22 3627.89 >> 44 P18 F N 45.49916004 297.1312253 160.4104035 635.12 1325.33 >> 45 P18 M N 10.83264523 179.2726374 39.85155791 64.24 763.59 >> 46 P18 M N 18.5827312 3389.23762 71.66394523 1105.37 45291.49 >> 47 P18 F N 7.416300711 1345.377837 29.62228101 1195.82 19241.32 >> 48 P18 M Y 4383 19.16634287 137.1490061 20.22826506 157.45 4026.95 >> 49 P18 M Y 4748.25 19.0830674 226.7358839 93.61453199 507.45 1274.6 >> 50 P18 M Y 4748.25 19.0830674 285.870034 60.87840486 330.91 586.98 >> 51 P18 M Y 3652.5 12.33297048 195.6870101 39.56741133 48.1 16561.4 >> 52 P18 F Y 4017.75 11.24970596 145.4550742 42.55095042 20.56 732.42 >> 53 P18 F Y 1461 3.999956195 385.813107 63.1515775 204.62 2347.46 >> 54 P18 M Y 4748.25 16.08310025 117.965944 58.03693906 78.33 2709.32 >> 55 P18 M Y 1826.25 13.99984668 175.9106574 67.41377621 65.53 2069.11 >> 56 P18 M Y 730.5 14.9158769 89.68575957 27.91740153 22.62 389.59 >> 57 P18 F Y 6209.25 17.4161912 191.9295031 32.60582011 127.63 20291.34 >> 58 P18 F Y 365.25 5.249771666 121.723451 61.7308446 49.39 11463.27 >> 59 P18 F Y 4748.25 18.33290477 179.0748739 53.20644719 46.16 >> 111361.43 >> 60 P18 M Y 1826.25 6.083209766 330.6801911 27.06496179 489.04 >> 12258.96 >> 61 P18 F Y 3287.25 17.58274215 182.8323809 29.48020772 115.1 15324.67 >> 62 P18 F Y 3652.5 44.16606909 248.4898719 87.24178099 139.33 16443.86 >> 63 P19 M N 37.99958385 2197.263844 86.43305867 1492.06 3547.88 >> 64 P19 F N 37.58252312 4588.403833 152.9115464 1722.46 9243.22 >> 65 P19 F N 34.91565787 316.0623502 17.19804354 1582.79 12217.62 >> 66 P19 F N 42.74901931 213.1054131 32.99689553 212.94 2714.66 >> 67 P19 F N 10.08316596 4715.658374 50.91906722 1543.61 2490.68 >> 68 P19 F N 43.33263099 2.258320699 0.524578302 561.12 5985.07 >> 69 P19 F Y 365.25 8.999901438 208.5132426 32.8293986 45.72 2051.68 >> 70 P19 M Y 4748.25 12.83262333 0 0 192.51 1255.58 >> 71 P19 M Y 1461 16.83257952 218.2716049 65.82629413 255.01 4486.39 >> 72 P19 M Y 5844 17.4161912 102.60631 27.80449065 49.77 622.01 >> 73 P19 M Y 4748.25 18.33290477 182.9692941 9.965221488 159.66 2392.13 >> 74 P19 F Y 730.5 17.24964025 100.8842461 27.97198758 157.25 176209.9 >> 75 P19 M Y 4383 16.41620215 0.098187856 0 171.67 65286.23 >> 76 P19 M Y 1461 6.16648524 962.1232959 112.1204345 81.67 870.82 >> >> >> >> > > -- > View this message in context: http://www.nabble.com/need-help-for-t.test-using-%22by%22-tp25035006p25043601.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.David Winsemius, MD Heritage Laboratories West Hartford, CT
Thanks for the reply, and sorry for not being clear, I have ELISA data for 50 plates, equal number of disease and control samples are located on each plates. I need to do the ttest between each proteins listed as prt1, prt2... prt50 on all the plates 1-50, however for some proteins i have data for 40 plates and that is creating the problem for me when I run "by(eo,eo$PlateID, function(.sub) t.test(prt1~Disease,data=.sub))". If i only take the data for 40 plates, this command works, unfortunately I do not want to make multiple copies of the same data over to do things. Similarly"by(eo,eo$sex,function(.sub) t.test(prt1~Disease,data=.sub))" is also not working when I select the data for 40 plates. I used these two formulas earlier sucessfully. I am uploading a part of data as a delim file for sample http://www.nabble.com/file/p25051220/r..txt r..txt . Thanks 1Rnwb wrote:> > any one > > 1Rnwb wrote: >> >> I am trying to do ttest for each plate which has equal number of disease >> and controls. by searching this forum I found one posting suggesting OP >> to use "by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub))". >> when i modified this for my use I used to get the pvalues for each plate, >> recently upgraded to R2.9.x and now i am getting following error when i >> use this >> > by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)) >> Error in t.test.formula(IL1Ra ~ Group, data = .sub) : >> grouping factor must have exactly 2 levels >> >> I checked my data file and the plate ID has "P16-P47" and the disease >> column is "Y/N". I have search all but could not locate the answer. Can >> anyone suggest me the direction where i am going wrong. >> for more detail i amm posting a part of my data. >> >> SampleID PlateID Sex Disease Duration Age prt1 prt2 prt3 prt4 >> 1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43 >> 2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36 >> 3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52 >> 4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04 >> 5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36 >> 6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75 >> 7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69 >> 8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61 >> 9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72 >> 10 P16 M N 0.916030215 242.3011559 36.40117263 90.1 35962.08 >> 11 P16 F Y 14975.25 42.08281552 133.8052501 29.0570764 260.55 1280.29 >> 12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6 >> 13 P16 F Y 2922 25.08300169 231.6043765 9.022844487 902.53 37571.39 >> 14 P16 F Y 12053.25 37.49924765 158.6370595 24.90606549 1.63 471.15 >> 15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49 >> 16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21 >> 17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27 >> 18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89 >> 19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15 >> 20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86 >> 21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47 >> 22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12 >> 23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78 >> 24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62 >> 25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14 >> 26 P17 M Y 12053.25 50.91548265 173.7764722 18.90280088 52.25 15962.05 >> 27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95 >> 28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39 >> 29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48 >> 30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83 >> 31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02 >> 32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84 >> 33 P17 M Y 8766 31.74913978 220.2561296 34.40329218 130.31 2377.36 >> 34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 19587.61 >> 35 P17 M Y 12053.25 36.1661567 212.1613578 96.51775947 621.42 3269.9 >> 36 P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27 >> 37 P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77 >> 38 P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32 248857.58 >> 39 P18 F N 14.2496731 538.5430144 54.34303351 396 4432.94 >> 40 P18 M N 11.83263428 236.8218238 48.37595532 148.94 1414.11 >> 41 P18 M N 7.582851659 322.2342976 87.83185053 280.84 16294.98 >> 42 P18 F N 8.83266713 288.4507237 30.47472075 256.38 348.03 >> 43 P18 M N 43.58245741 297.1312253 3.276042927 368.22 3627.89 >> 44 P18 F N 45.49916004 297.1312253 160.4104035 635.12 1325.33 >> 45 P18 M N 10.83264523 179.2726374 39.85155791 64.24 763.59 >> 46 P18 M N 18.5827312 3389.23762 71.66394523 1105.37 45291.49 >> 47 P18 F N 7.416300711 1345.377837 29.62228101 1195.82 19241.32 >> 48 P18 M Y 4383 19.16634287 137.1490061 20.22826506 157.45 4026.95 >> 49 P18 M Y 4748.25 19.0830674 226.7358839 93.61453199 507.45 1274.6 >> 50 P18 M Y 4748.25 19.0830674 285.870034 60.87840486 330.91 586.98 >> 51 P18 M Y 3652.5 12.33297048 195.6870101 39.56741133 48.1 16561.4 >> 52 P18 F Y 4017.75 11.24970596 145.4550742 42.55095042 20.56 732.42 >> 53 P18 F Y 1461 3.999956195 385.813107 63.1515775 204.62 2347.46 >> 54 P18 M Y 4748.25 16.08310025 117.965944 58.03693906 78.33 2709.32 >> 55 P18 M Y 1826.25 13.99984668 175.9106574 67.41377621 65.53 2069.11 >> 56 P18 M Y 730.5 14.9158769 89.68575957 27.91740153 22.62 389.59 >> 57 P18 F Y 6209.25 17.4161912 191.9295031 32.60582011 127.63 20291.34 >> 58 P18 F Y 365.25 5.249771666 121.723451 61.7308446 49.39 11463.27 >> 59 P18 F Y 4748.25 18.33290477 179.0748739 53.20644719 46.16 111361.43 >> 60 P18 M Y 1826.25 6.083209766 330.6801911 27.06496179 489.04 12258.96 >> 61 P18 F Y 3287.25 17.58274215 182.8323809 29.48020772 115.1 15324.67 >> 62 P18 F Y 3652.5 44.16606909 248.4898719 87.24178099 139.33 16443.86 >> 63 P19 M N 37.99958385 2197.263844 86.43305867 1492.06 3547.88 >> 64 P19 F N 37.58252312 4588.403833 152.9115464 1722.46 9243.22 >> 65 P19 F N 34.91565787 316.0623502 17.19804354 1582.79 12217.62 >> 66 P19 F N 42.74901931 213.1054131 32.99689553 212.94 2714.66 >> 67 P19 F N 10.08316596 4715.658374 50.91906722 1543.61 2490.68 >> 68 P19 F N 43.33263099 2.258320699 0.524578302 561.12 5985.07 >> 69 P19 F Y 365.25 8.999901438 208.5132426 32.8293986 45.72 2051.68 >> 70 P19 M Y 4748.25 12.83262333 0 0 192.51 1255.58 >> 71 P19 M Y 1461 16.83257952 218.2716049 65.82629413 255.01 4486.39 >> 72 P19 M Y 5844 17.4161912 102.60631 27.80449065 49.77 622.01 >> 73 P19 M Y 4748.25 18.33290477 182.9692941 9.965221488 159.66 2392.13 >> 74 P19 F Y 730.5 17.24964025 100.8842461 27.97198758 157.25 176209.9 >> 75 P19 M Y 4383 16.41620215 0.098187856 0 171.67 65286.23 >> 76 P19 M Y 1461 6.16648524 962.1232959 112.1204345 81.67 870.82 >> >> >> >> > >-- View this message in context: http://www.nabble.com/need-help-for-t.test-using-%22by%22-tp25035006p25051220.html Sent from the R help mailing list archive at Nabble.com.