Hi everybody, this is a real dummy thing.
I sorted a matrix based on a given column, and what I get is right, until it
comes to columns of negative and positive values; than, "order" orders
everything from max to min in the negative values, and then AGAIN from max to
min in the positive values!!!
Why isn't everything order from max to min, and that's it?
Thank you!!!
Attached is the txt file I use; try:
x=x[order(x[,2]),]
What I get is:
print(x)
Product A B Tissue
44 ME:MDA_MB_435 -0.1915 -0.16744 Melanoma
17 CNS:SNB_75 -0.23183 1.03945 CNS
37 LE:K_562 -0.58218 1.8581 Leukemia
43 ME:MALME_3M -0.67327 -1.33493 Melanoma
49 ME:UACC_257 -0.72431 -1.84753 Melanoma
42 ME:M14 -0.73942 -0.73904 Melanoma
40 LE:SR -0.93541 2.95346 Leukemia
25 CO:SW_620 -1.53265 -1.35446 Colon
63 RE:CAKI_1 -2.48443 0.43245 Renal
39 LE:RPMI_8226 -2.59561 -1.9448 Leukemia
26 LC:A549 -2.66221 0.71215 Lung
61 RE:A498 -2.89402 0.93287 Renal
9 BR:HS578T -2.94118 1.1217 Breast
34 LC:NCI_H522 -2.94381 0.3859 Lung
66 RE:TK_10 -2.95281 1.26245 Renal
52 OV:NCI_ADR_RES -3.04456 0.17046 Ovarian
57 OV:SK_OV_3 -3.04477 2.15405 Ovarian
53 OV:OVCAR_3 -3.0705 -0.31743 Ovarian
14 CNS:SF_295 -3.09348 -1.00095 CNS
54 OV:OVCAR_4 -3.13137 -0.47497 Ovarian
36 LE:HL_60 -3.16745 -3.16745 Leukemia
38 LE:MOLT_4 -3.20055 -1.72841 Leukemia
11 BR:MDA_MB_231 -3.24907 1.58326 Breast
59 PR:PC_3 -3.36612 1.39328 Prostate
19 CO:HCT_116 -3.39764 0.43061 Colon
12 BR:T47D -3.41228 1.13818 Breast
22 CO:HCT_15 -3.45342 0.16357 Colon
64 RE:RXF_393 -3.49615 2.59144 Renal
28 LC:HOP_62 -3.4968 0.67884 Lung
60 RE:786_0 -3.5086 1.75056 Renal
35 LE:CCRF_CEM -3.54526 -2.09262 Leukemia
29 LC:HOP_92 -3.60636 0.87116 Lung
21 CO:HCC_2998 -3.61457 -0.32362 Colon
13 CNS:SF_268 -3.63916 2.54378 CNS
20 CO:COLO205 -3.64656 0.54344 Colon
56 OV:OVCAR_8 -3.66053 -0.9594 Ovarian
24 CO:KM12 -3.68703 2.19991 Colon
55 OV:OVCAR_5 -3.7852 2.43038 Ovarian
8 BR:BT_549 -3.80239 -0.43099 Breast
15 CNS:SF_539 -3.86184 1.39114 CNS
65 RE:SN12C -3.90776 0.85244 Renal
31 LC:NCI_H23 -3.91625 -1.14955 Lung
62 RE:ACHN -3.96246 -0.62365 Renal
67 RE:UO_31 -3.99791 -1.09215 Renal
10 BR:MCF7 -4.00187 1.46303 Breast
51 OV:IGROV1 -4.02758 2.04324 Ovarian
23 CO:HT29 -4.11624 -0.02799 Colon
41 ME:LOXIMVI -4.2572 0.37259 Melanoma
32 LC:NCI_H322M -4.28534 1.66783 Lung
27 LC:EKVX -4.32847 1.66042 Lung
58 PR:DU_145 -4.33961 1.57548 Prostate
30 LC:NCI_H226 -4.37408 -0.22311 Lung
33 LC:NCI_H460 0.0042 -0.6023 Lung
18 CNS:U251 0.01263 1.66389 CNS
16 CNS:SNB_19 0.16583 0.03737 CNS
45 ME:MDA_N 0.21077 0.05502 Melanoma
50 ME:UACC_62 0.52503 0.1605 Melanoma
46 ME:SK_MEL_2 0.55255 -1.6667 Melanoma
47 ME:SK_MEL_28 1.7425 1.45266 Melanoma
48 ME:SK_MEL_5 1.74749 -1.47817 Melanoma
Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of
Genova, Genova, Italy
Guest Researcher, LMP, NCI, NIH, Bethesda MD
Work: 301-451-8575
Mobile: 301-204-5642
Email: zoppolig at mail.nih.gov
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do 'str' on your object to see if you have factors where you think you have numerics. What is the problem you are trying to solve? Sent from my iPhone. On May 23, 2010, at 17:39, "Zoppoli, Gabriele (NIH/NCI) [G]" <zoppolig at mail.nih.gov > wrote:> Hi everybody, this is a real dummy thing. > > I sorted a matrix based on a given column, and what I get is right, > until it comes to columns of negative and positive values; than, > "order" orders everything from max to min in the negative values, > and then AGAIN from max to min in the positive values!!! > > Why isn't everything order from max to min, and that's it? > > Thank you!!! > > Attached is the txt file I use; try: > > x=x[order(x[,2]),] > > What I get is: > > print(x) > > > Product A B Tissue > 44 ME:MDA_MB_435 -0.1915 -0.16744 Melanoma > 17 CNS:SNB_75 -0.23183 1.03945 CNS > 37 LE:K_562 -0.58218 1.8581 Leukemia > 43 ME:MALME_3M -0.67327 -1.33493 Melanoma > 49 ME:UACC_257 -0.72431 -1.84753 Melanoma > 42 ME:M14 -0.73942 -0.73904 Melanoma > 40 LE:SR -0.93541 2.95346 Leukemia > 25 CO:SW_620 -1.53265 -1.35446 Colon > 63 RE:CAKI_1 -2.48443 0.43245 Renal > 39 LE:RPMI_8226 -2.59561 -1.9448 Leukemia > 26 LC:A549 -2.66221 0.71215 Lung > 61 RE:A498 -2.89402 0.93287 Renal > 9 BR:HS578T -2.94118 1.1217 Breast > 34 LC:NCI_H522 -2.94381 0.3859 Lung > 66 RE:TK_10 -2.95281 1.26245 Renal > 52 OV:NCI_ADR_RES -3.04456 0.17046 Ovarian > 57 OV:SK_OV_3 -3.04477 2.15405 Ovarian > 53 OV:OVCAR_3 -3.0705 -0.31743 Ovarian > 14 CNS:SF_295 -3.09348 -1.00095 CNS > 54 OV:OVCAR_4 -3.13137 -0.47497 Ovarian > 36 LE:HL_60 -3.16745 -3.16745 Leukemia > 38 LE:MOLT_4 -3.20055 -1.72841 Leukemia > 11 BR:MDA_MB_231 -3.24907 1.58326 Breast > 59 PR:PC_3 -3.36612 1.39328 Prostate > 19 CO:HCT_116 -3.39764 0.43061 Colon > 12 BR:T47D -3.41228 1.13818 Breast > 22 CO:HCT_15 -3.45342 0.16357 Colon > 64 RE:RXF_393 -3.49615 2.59144 Renal > 28 LC:HOP_62 -3.4968 0.67884 Lung > 60 RE:786_0 -3.5086 1.75056 Renal > 35 LE:CCRF_CEM -3.54526 -2.09262 Leukemia > 29 LC:HOP_92 -3.60636 0.87116 Lung > 21 CO:HCC_2998 -3.61457 -0.32362 Colon > 13 CNS:SF_268 -3.63916 2.54378 CNS > 20 CO:COLO205 -3.64656 0.54344 Colon > 56 OV:OVCAR_8 -3.66053 -0.9594 Ovarian > 24 CO:KM12 -3.68703 2.19991 Colon > 55 OV:OVCAR_5 -3.7852 2.43038 Ovarian > 8 BR:BT_549 -3.80239 -0.43099 Breast > 15 CNS:SF_539 -3.86184 1.39114 CNS > 65 RE:SN12C -3.90776 0.85244 Renal > 31 LC:NCI_H23 -3.91625 -1.14955 Lung > 62 RE:ACHN -3.96246 -0.62365 Renal > 67 RE:UO_31 -3.99791 -1.09215 Renal > 10 BR:MCF7 -4.00187 1.46303 Breast > 51 OV:IGROV1 -4.02758 2.04324 Ovarian > 23 CO:HT29 -4.11624 -0.02799 Colon > 41 ME:LOXIMVI -4.2572 0.37259 Melanoma > 32 LC:NCI_H322M -4.28534 1.66783 Lung > 27 LC:EKVX -4.32847 1.66042 Lung > 58 PR:DU_145 -4.33961 1.57548 Prostate > 30 LC:NCI_H226 -4.37408 -0.22311 Lung > 33 LC:NCI_H460 0.0042 -0.6023 Lung > 18 CNS:U251 0.01263 1.66389 CNS > 16 CNS:SNB_19 0.16583 0.03737 CNS > 45 ME:MDA_N 0.21077 0.05502 Melanoma > 50 ME:UACC_62 0.52503 0.1605 Melanoma > 46 ME:SK_MEL_2 0.55255 -1.6667 Melanoma > 47 ME:SK_MEL_28 1.7425 1.45266 Melanoma > 48 ME:SK_MEL_5 1.74749 -1.47817 Melanoma > > Gabriele Zoppoli, MD > Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, > University of Genova, Genova, Italy > Guest Researcher, LMP, NCI, NIH, Bethesda MD > > Work: 301-451-8575 > Mobile: 301-204-5642 > Email: zoppolig at mail.nih.gov > <x.txt> > ______________________________________________ > 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.
I tried this, but it doesn't change the "division" between negative and positive values (see that you have first positive from max to min, and then negative from min to max, as if "order" considered only the absolute values...) Product hsa.miR.204 hsa.miR.210 Tissue 48 "ME:SK_MEL_5" "1.74749" "-1.47817" "Melanoma" 47 "ME:SK_MEL_28" "1.7425" "1.45266" "Melanoma" 46 "ME:SK_MEL_2" "0.55255" "-1.6667" "Melanoma" 50 "ME:UACC_62" "0.52503" "0.1605" "Melanoma" 45 "ME:MDA_N" "0.21077" "0.05502" "Melanoma" 16 "CNS:SNB_19" "0.16583" "0.03737" "CNS" 18 "CNS:U251" "0.01263" "1.66389" "CNS" 33 "LC:NCI_H460" "0.0042" "-0.6023" "Lung" 30 "LC:NCI_H226" "-4.37408" "-0.22311" "Lung" 58 "PR:DU_145" "-4.33961" "1.57548" "Prostate" 27 "LC:EKVX" "-4.32847" "1.66042" "Lung" 32 "LC:NCI_H322M" "-4.28534" "1.66783" "Lung" 41 "ME:LOXIMVI" "-4.2572" "0.37259" "Melanoma" 23 "CO:HT29" "-4.11624" "-0.02799" "Colon" 51 "OV:IGROV1" "-4.02758" "2.04324" "Ovarian" 10 "BR:MCF7" "-4.00187" "1.46303" "Breast" 67 "RE:UO_31" "-3.99791" "-1.09215" "Renal" 62 "RE:ACHN" "-3.96246" "-0.62365" "Renal" 31 "LC:NCI_H23" "-3.91625" "-1.14955" "Lung" 65 "RE:SN12C" "-3.90776" "0.85244" "Renal" 15 "CNS:SF_539" "-3.86184" "1.39114" "CNS" 8 "BR:BT_549" "-3.80239" "-0.43099" "Breast" 55 "OV:OVCAR_5" "-3.7852" "2.43038" "Ovarian" 24 "CO:KM12" "-3.68703" "2.19991" "Colon" 56 "OV:OVCAR_8" "-3.66053" "-0.9594" "Ovarian" 20 "CO:COLO205" "-3.64656" "0.54344" "Colon" 13 "CNS:SF_268" "-3.63916" "2.54378" "CNS" 21 "CO:HCC_2998" "-3.61457" "-0.32362" "Colon" 29 "LC:HOP_92" "-3.60636" "0.87116" "Lung" 35 "LE:CCRF_CEM" "-3.54526" "-2.09262" "Leukemia" 60 "RE:786_0" "-3.5086" "1.75056" "Renal" 28 "LC:HOP_62" "-3.4968" "0.67884" "Lung" 64 "RE:RXF_393" "-3.49615" "2.59144" "Renal" 22 "CO:HCT_15" "-3.45342" "0.16357" "Colon" 12 "BR:T47D" "-3.41228" "1.13818" "Breast" 19 "CO:HCT_116" "-3.39764" "0.43061" "Colon" 59 "PR:PC_3" "-3.36612" "1.39328" "Prostate" 11 "BR:MDA_MB_231" "-3.24907" "1.58326" "Breast" 38 "LE:MOLT_4" "-3.20055" "-1.72841" "Leukemia" 36 "LE:HL_60" "-3.16745" "-3.16745" "Leukemia" 54 "OV:OVCAR_4" "-3.13137" "-0.47497" "Ovarian" 14 "CNS:SF_295" "-3.09348" "-1.00095" "CNS" 53 "OV:OVCAR_3" "-3.0705" "-0.31743" "Ovarian" 57 "OV:SK_OV_3" "-3.04477" "2.15405" "Ovarian" 52 "OV:NCI_ADR_RES" "-3.04456" "0.17046" "Ovarian" 66 "RE:TK_10" "-2.95281" "1.26245" "Renal" 34 "LC:NCI_H522" "-2.94381" "0.3859" "Lung" 9 "BR:HS578T" "-2.94118" "1.1217" "Breast" 61 "RE:A498" "-2.89402" "0.93287" "Renal" 26 "LC:A549" "-2.66221" "0.71215" "Lung" 39 "LE:RPMI_8226" "-2.59561" "-1.9448" "Leukemia" 63 "RE:CAKI_1" "-2.48443" "0.43245" "Renal" 25 "CO:SW_620" "-1.53265" "-1.35446" "Colon" 40 "LE:SR" "-0.93541" "2.95346" "Leukemia" 42 "ME:M14" "-0.73942" "-0.73904" "Melanoma" 49 "ME:UACC_257" "-0.72431" "-1.84753" "Melanoma" 43 "ME:MALME_3M" "-0.67327" "-1.33493" "Melanoma" 37 "LE:K_562" "-0.58218" "1.8581" "Leukemia" 17 "CNS:SNB_75" "-0.23183" "1.03945" "CNS" 44 "ME:MDA_MB_435" "-0.1915" "-0.16744" "Melanoma" Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov ________________________________________ From: Jorge Ivan Velez [jorgeivanvelez at gmail.com] Sent: Sunday, May 23, 2010 6:09 PM To: Zoppoli, Gabriele (NIH/NCI) [G] Subject: Re: [R] "order" issue Hi Gabriele, Take a look at the "decreasing" argument in ?order> xx <-c(1,3,4,10, 5,2,3,8,9) > xx[1] 1 3 4 10 5 2 3 8 9> xx[order(xx)][1] 1 2 3 3 4 5 8 9 10> xx[order(xx, decreasing = TRUE)][1] 10 9 8 5 4 3 3 2 1 HTH, Jorge On Sun, May 23, 2010 at 5:39 PM, Zoppoli, Gabriele (NIH/NCI) [G] <zoppolig at mail.nih.gov<mailto:zoppolig at mail.nih.gov>> wrote: Hi everybody, this is a real dummy thing. I sorted a matrix based on a given column, and what I get is right, until it comes to columns of negative and positive values; than, "order" orders everything from max to min in the negative values, and then AGAIN from max to min in the positive values!!! Why isn't everything order from max to min, and that's it? Thank you!!! Attached is the txt file I use; try: x=x[order(x[,2]),] What I get is: print(x) Product A B Tissue 44 ME:MDA_MB_435 -0.1915 -0.16744 Melanoma 17 CNS:SNB_75 -0.23183 1.03945 CNS 37 LE:K_562 -0.58218 1.8581 Leukemia 43 ME:MALME_3M -0.67327 -1.33493 Melanoma 49 ME:UACC_257 -0.72431 -1.84753 Melanoma 42 ME:M14 -0.73942 -0.73904 Melanoma 40 LE:SR -0.93541 2.95346 Leukemia 25 CO:SW_620 -1.53265 -1.35446 Colon 63 RE:CAKI_1 -2.48443 0.43245 Renal 39 LE:RPMI_8226 -2.59561 -1.9448 Leukemia 26 LC:A549 -2.66221 0.71215 Lung 61 RE:A498 -2.89402 0.93287 Renal 9 BR:HS578T -2.94118 1.1217 Breast 34 LC:NCI_H522 -2.94381 0.3859 Lung 66 RE:TK_10 -2.95281 1.26245 Renal 52 OV:NCI_ADR_RES -3.04456 0.17046 Ovarian 57 OV:SK_OV_3 -3.04477 2.15405 Ovarian 53 OV:OVCAR_3 -3.0705 -0.31743 Ovarian 14 CNS:SF_295 -3.09348 -1.00095 CNS 54 OV:OVCAR_4 -3.13137 -0.47497 Ovarian 36 LE:HL_60 -3.16745 -3.16745 Leukemia 38 LE:MOLT_4 -3.20055 -1.72841 Leukemia 11 BR:MDA_MB_231 -3.24907 1.58326 Breast 59 PR:PC_3 -3.36612 1.39328 Prostate 19 CO:HCT_116 -3.39764 0.43061 Colon 12 BR:T47D -3.41228 1.13818 Breast 22 CO:HCT_15 -3.45342 0.16357 Colon 64 RE:RXF_393 -3.49615 2.59144 Renal 28 LC:HOP_62 -3.4968 0.67884 Lung 60 RE:786_0 -3.5086 1.75056 Renal 35 LE:CCRF_CEM -3.54526 -2.09262 Leukemia 29 LC:HOP_92 -3.60636 0.87116 Lung 21 CO:HCC_2998 -3.61457 -0.32362 Colon 13 CNS:SF_268 -3.63916 2.54378 CNS 20 CO:COLO205 -3.64656 0.54344 Colon 56 OV:OVCAR_8 -3.66053 -0.9594 Ovarian 24 CO:KM12 -3.68703 2.19991 Colon 55 OV:OVCAR_5 -3.7852 2.43038 Ovarian 8 BR:BT_549 -3.80239 -0.43099 Breast 15 CNS:SF_539 -3.86184 1.39114 CNS 65 RE:SN12C -3.90776 0.85244 Renal 31 LC:NCI_H23 -3.91625 -1.14955 Lung 62 RE:ACHN -3.96246 -0.62365 Renal 67 RE:UO_31 -3.99791 -1.09215 Renal 10 BR:MCF7 -4.00187 1.46303 Breast 51 OV:IGROV1 -4.02758 2.04324 Ovarian 23 CO:HT29 -4.11624 -0.02799 Colon 41 ME:LOXIMVI -4.2572 0.37259 Melanoma 32 LC:NCI_H322M -4.28534 1.66783 Lung 27 LC:EKVX -4.32847 1.66042 Lung 58 PR:DU_145 -4.33961 1.57548 Prostate 30 LC:NCI_H226 -4.37408 -0.22311 Lung 33 LC:NCI_H460 0.0042 -0.6023 Lung 18 CNS:U251 0.01263 1.66389 CNS 16 CNS:SNB_19 0.16583 0.03737 CNS 45 ME:MDA_N 0.21077 0.05502 Melanoma 50 ME:UACC_62 0.52503 0.1605 Melanoma 46 ME:SK_MEL_2 0.55255 -1.6667 Melanoma 47 ME:SK_MEL_28 1.7425 1.45266 Melanoma 48 ME:SK_MEL_5 1.74749 -1.47817 Melanoma Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppolig at mail.nih.gov<mailto:zoppolig at mail.nih.gov> ______________________________________________ R-help at r-project.org<mailto: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.
On 23-May-10 21:39:06, Zoppoli, Gabriele (NIH/NCI) [G] wrote:> Hi everybody, this is a real dummy thing. > > I sorted a matrix based on a given column, and what I get is right, > until it comes to columns of negative and positive values; than, > "order" orders everything from max to min in the negative values, and > then AGAIN from max to min in the positive values!!! > > Why isn't everything order from max to min, and that's it? > Thank you!!! > > Attached is the txt file I use; try: > > x=x[order(x[,2]),] > > What I get is: > > print(x) > > Product A B Tissue > 44 ME:MDA_MB_435 -0.1915 -0.16744 Melanoma > 17 CNS:SNB_75 -0.23183 1.03945 CNS > 37 LE:K_562 -0.58218 1.8581 Leukemia > 43 ME:MALME_3M -0.67327 -1.33493 Melanoma > 49 ME:UACC_257 -0.72431 -1.84753 Melanoma > 42 ME:M14 -0.73942 -0.73904 Melanoma > 40 LE:SR -0.93541 2.95346 Leukemia > 25 CO:SW_620 -1.53265 -1.35446 Colon > 63 RE:CAKI_1 -2.48443 0.43245 Renal > 39 LE:RPMI_8226 -2.59561 -1.9448 Leukemia > 26 LC:A549 -2.66221 0.71215 Lung > 61 RE:A498 -2.89402 0.93287 Renal > 9 BR:HS578T -2.94118 1.1217 Breast > 34 LC:NCI_H522 -2.94381 0.3859 Lung > 66 RE:TK_10 -2.95281 1.26245 Renal > 52 OV:NCI_ADR_RES -3.04456 0.17046 Ovarian > 57 OV:SK_OV_3 -3.04477 2.15405 Ovarian > 53 OV:OVCAR_3 -3.0705 -0.31743 Ovarian > 14 CNS:SF_295 -3.09348 -1.00095 CNS > 54 OV:OVCAR_4 -3.13137 -0.47497 Ovarian > 36 LE:HL_60 -3.16745 -3.16745 Leukemia > 38 LE:MOLT_4 -3.20055 -1.72841 Leukemia > 11 BR:MDA_MB_231 -3.24907 1.58326 Breast > 59 PR:PC_3 -3.36612 1.39328 Prostate > 19 CO:HCT_116 -3.39764 0.43061 Colon > 12 BR:T47D -3.41228 1.13818 Breast > 22 CO:HCT_15 -3.45342 0.16357 Colon > 64 RE:RXF_393 -3.49615 2.59144 Renal > 28 LC:HOP_62 -3.4968 0.67884 Lung > 60 RE:786_0 -3.5086 1.75056 Renal > 35 LE:CCRF_CEM -3.54526 -2.09262 Leukemia > 29 LC:HOP_92 -3.60636 0.87116 Lung > 21 CO:HCC_2998 -3.61457 -0.32362 Colon > 13 CNS:SF_268 -3.63916 2.54378 CNS > 20 CO:COLO205 -3.64656 0.54344 Colon > 56 OV:OVCAR_8 -3.66053 -0.9594 Ovarian > 24 CO:KM12 -3.68703 2.19991 Colon > 55 OV:OVCAR_5 -3.7852 2.43038 Ovarian > 8 BR:BT_549 -3.80239 -0.43099 Breast > 15 CNS:SF_539 -3.86184 1.39114 CNS > 65 RE:SN12C -3.90776 0.85244 Renal > 31 LC:NCI_H23 -3.91625 -1.14955 Lung > 62 RE:ACHN -3.96246 -0.62365 Renal > 67 RE:UO_31 -3.99791 -1.09215 Renal > 10 BR:MCF7 -4.00187 1.46303 Breast > 51 OV:IGROV1 -4.02758 2.04324 Ovarian > 23 CO:HT29 -4.11624 -0.02799 Colon > 41 ME:LOXIMVI -4.2572 0.37259 Melanoma > 32 LC:NCI_H322M -4.28534 1.66783 Lung > 27 LC:EKVX -4.32847 1.66042 Lung > 58 PR:DU_145 -4.33961 1.57548 Prostate > 30 LC:NCI_H226 -4.37408 -0.22311 Lung > 33 LC:NCI_H460 0.0042 -0.6023 Lung > 18 CNS:U251 0.01263 1.66389 CNS > 16 CNS:SNB_19 0.16583 0.03737 CNS > 45 ME:MDA_N 0.21077 0.05502 Melanoma > 50 ME:UACC_62 0.52503 0.1605 Melanoma > 46 ME:SK_MEL_2 0.55255 -1.6667 Melanoma > 47 ME:SK_MEL_28 1.7425 1.45266 Melanoma > 48 ME:SK_MEL_5 1.74749 -1.47817 Melanoma > > Gabriele Zoppoli, MDSomewhat strange indeed! The only further question I can think of is to ask how what did "x" look like before your re-ordered it. Using the "x.txt" file you supplied, I get: x <- read.table("x.txt") str(x) # 'data.frame': 60 obs. of 4 variables: # $ Product: Factor w/ 60 levels "BR:BT_549","BR:HS578T",..: 37 10 30 # 36 42 35 33 18 56 32 ... # $ A : num -0.192 -0.232 -0.582 -0.673 -0.724 ... # $ B : num -0.167 1.039 1.858 -1.335 -1.848 ... # $ Tissue : Factor w/ 9 levels "Breast","CNS",..: 6 2 4 6 6 6 4 3 9 4 # ... so x[,2] and x[,3] are indeed numeric. Then (similar to yours): X<-x[order(x[,2]),] print(X) # Product A B Tissue # 30 LC:NCI_H226 -4.37408 -0.22311 Lung # 58 PR:DU_145 -4.33961 1.57548 Prostate # 27 LC:EKVX -4.32847 1.66042 Lung # 32 LC:NCI_H322M -4.28534 1.66783 Lung # 41 ME:LOXIMVI -4.25720 0.37259 Melanoma # 23 CO:HT29 -4.11624 -0.02799 Colon # 51 OV:IGROV1 -4.02758 2.04324 Ovarian # 10 BR:MCF7 -4.00187 1.46303 Breast # 67 RE:UO_31 -3.99791 -1.09215 Renal # 62 RE:ACHN -3.96246 -0.62365 Renal # 31 LC:NCI_H23 -3.91625 -1.14955 Lung # 65 RE:SN12C -3.90776 0.85244 Renal # 15 CNS:SF_539 -3.86184 1.39114 CNS # 8 BR:BT_549 -3.80239 -0.43099 Breast # 55 OV:OVCAR_5 -3.78520 2.43038 Ovarian # 24 CO:KM12 -3.68703 2.19991 Colon # 56 OV:OVCAR_8 -3.66053 -0.95940 Ovarian # 20 CO:COLO205 -3.64656 0.54344 Colon # 13 CNS:SF_268 -3.63916 2.54378 CNS # 21 CO:HCC_2998 -3.61457 -0.32362 Colon # 29 LC:HOP_92 -3.60636 0.87116 Lung # 35 LE:CCRF_CEM -3.54526 -2.09262 Leukemia # 60 RE:786_0 -3.50860 1.75056 Renal # 28 LC:HOP_62 -3.49680 0.67884 Lung # 64 RE:RXF_393 -3.49615 2.59144 Renal # 22 CO:HCT_15 -3.45342 0.16357 Colon # 12 BR:T47D -3.41228 1.13818 Breast # 19 CO:HCT_116 -3.39764 0.43061 Colon # 59 PR:PC_3 -3.36612 1.39328 Prostate # 11 BR:MDA_MB_231 -3.24907 1.58326 Breast # 38 LE:MOLT_4 -3.20055 -1.72841 Leukemia # 36 LE:HL_60 -3.16745 -3.16745 Leukemia # 54 OV:OVCAR_4 -3.13137 -0.47497 Ovarian # 14 CNS:SF_295 -3.09348 -1.00095 CNS # 53 OV:OVCAR_3 -3.07050 -0.31743 Ovarian # 57 OV:SK_OV_3 -3.04477 2.15405 Ovarian # 52 OV:NCI_ADR_RES -3.04456 0.17046 Ovarian # 66 RE:TK_10 -2.95281 1.26245 Renal # 34 LC:NCI_H522 -2.94381 0.38590 Lung # 9 BR:HS578T -2.94118 1.12170 Breast # 61 RE:A498 -2.89402 0.93287 Renal # 26 LC:A549 -2.66221 0.71215 Lung # 39 LE:RPMI_8226 -2.59561 -1.94480 Leukemia # 63 RE:CAKI_1 -2.48443 0.43245 Renal # 25 CO:SW_620 -1.53265 -1.35446 Colon # 40 LE:SR -0.93541 2.95346 Leukemia # 42 ME:M14 -0.73942 -0.73904 Melanoma # 49 ME:UACC_257 -0.72431 -1.84753 Melanoma # 43 ME:MALME_3M -0.67327 -1.33493 Melanoma # 37 LE:K_562 -0.58218 1.85810 Leukemia # 17 CNS:SNB_75 -0.23183 1.03945 CNS # 44 ME:MDA_MB_435 -0.19150 -0.16744 Melanoma # 33 LC:NCI_H460 0.00420 -0.60230 Lung # 18 CNS:U251 0.01263 1.66389 CNS # 16 CNS:SNB_19 0.16583 0.03737 CNS # 45 ME:MDA_N 0.21077 0.05502 Melanoma # 50 ME:UACC_62 0.52503 0.16050 Melanoma # 46 ME:SK_MEL_2 0.55255 -1.66670 Melanoma # 47 ME:SK_MEL_28 1.74250 1.45266 Melanoma # 48 ME:SK_MEL_5 1.74749 -1.47817 Melanoma and now the values in X[,2] are indeed in the correct numerical order, yet essentially the same command as your has been executed. I have not succeeded in repoducing your result by ordering on other columns of "x" or on the row-names of "x". So it is a mystery! The only thing I can think of is that the columns of "x" (as seen by R) are different from what you think they should be. Since your file "x.txt" looks like the value of "x" after your re-ordering, it is impossible to test such guesses on the original "x". Ted. -------------------------------------------------------------------- E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk> Fax-to-email: +44 (0)870 094 0861 Date: 23-May-10 Time: 23:31:25 ------------------------------ XFMail ------------------------------