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...day 29 language R > test3 sj030110 sj030111 sj030112 control.ppm AFFX-DapX-M_at 216 236 227 13.3 AFFX-DapX-5_at 97 114 108 6.7 AFFX-CreX-5_at 1107 1021 1661 166.7 AFFX-BioB-5_at 595 511 772 83.3 AFFX-BioDn-3_at 3505 3059 4646 666.7 AFFX-BioB-3_at 2691 2310 3651 500.0 AFFX-CreX-3_at 189 198 262 20.0 AFFX-BioC-5_at 97 82 134 10.0 AFFX-BioC-3_at 286 236...

Thanks a lot, James!! The problem is fixed. On the version 1.4.0 Mac/darwin (the latest available version for this system) the function read.table (which is called from read.delim etc., too) has the bug you explained. Inserting the row nlines <- nlines+1 after lines <- c(lines, line) removes this bug. M. On Friday, February 22, 2002, at 02:33 PM, james.holtman at convergys.com

...data without any error Now if I use edit(mydata) It shows only 3916 entries, whereas the actual file contains 7129 entries) My data is something like Gene Description Gene Accession Number 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 34 35 36 37 38 28 29 30 31 32 33 AFFX-BioB-5_at (endogenous control) AFFX-BioB-5_at -214 -139 -76 -135 -106 -138 -72 -413 5 -88 -165 -67 -92 -113 -107 -117 -476 -81 -44 17 -144 -247 -74 -120 -81 -112 -273 -20 7 -213 -25 -72 -4 15 -318 -32 -124 -135 So it seems R is truncating the data. How can I load the complete file? Thanks in advance Di...

Hi, I use write.table() to write a file to an external xls file. the column names left-shift one position in output file. I check with col.names() row.names(), the file is fine. How to prevent the shifting? I71 I111 I304 I307 I305 I306 I114 I72 AFFX-BioB-5_at 6.66435 6.787807 5.335962 5.250163 6.47423 5.882104 5.965109 6.591687195 AFFX-BioB-M_at 6.163227 5.965427 4.665569 2.743531 6.097244 5.77137 5.113683 6.314003982 Thanks, Johnny [[alternative HTML version deleted]]

...elow to see if any gene(column 1 stands for gene names) is differentially expressed after subjecting it to the 6 different experiments(columns 2 to 7 are experiments). Gene 14A_U133A_Detection 14B_U133A_Signal 88A_U133A_Signal 88B_U133A_Signal 183A_U133A_Signal 183B_U133A_Signal AFFX-BioB-5_at 403 409.3 611.5 569.2 536.6 580.2 AFFX-BioB-M_at 757.3 574.4 826.7 595.3 755.2 956 AFFX-BioB-3_at 284.4 327.3 421.6 336.6 391.3 412.6 AFFX-BioC-5_at 2314.2 1685.3 2264.7 2204.1 2233.1 2458.4 AFFX-BioC-3_at 1574.5 1273 1484.6 1321.2 1474.7 1774.1 AFFX-BioDn-5_...

I have a data frame which has the following data. data<-read.table("table.txt",header=TRUE) data X14A_U133A_StatPairs X14A_U133A_Detection X14B_U133A_Signal 1 AFFX-BioB-5_at 403.0 409.3 2 AFFX-BioB-M_at 757.3 574.4 3 AFFX-BioB-3_at 284.4 327.3 4 AFFX-BioC-5_at 2314.2 1685.3 5 AFFX-BioC-3_at 1574.5 1273.0 6...

...ttribue in read.table and still make the colnames and coldata point to the same col#. Please suggest a solution. Thanks, Vasu. -------------- next part -------------- 14A_U133A_StatPairs 14A_U133A_Detection 14B_U133A_Signal 88A_U133A_Signal 88B_U133A_Signal 183A_U133A_Signal 183B_U133A_Signal AFFX-BioB-5_at 403.0 409.3 611.5 569.2 536.6 580.2 AFFX-BioB-M_at 757.3 574.4 826.7 595.3 755.2 956.0 AFFX-BioB-3_at 284.4 327.3 421.6 336.6 391.3 412.6 AFFX-BioC-5_at 2314.2 1685.3 2264.7 2204.1 2233.1 2458.4 AFFX-BioC-3_at 1574.5 1273.0 1484.6 1321.2 1474.7 1774.1 AFFX-BioDn-5_at 2333.7 1796.8 2464.5...

...ttribue in read.table and still make the colnames and coldata point to the same col#. Please suggest a solution. Thanks, Vasu. -------------- next part -------------- 14A_U133A_StatPairs 14A_U133A_Detection 14B_U133A_Signal 88A_U133A_Signal 88B_U133A_Signal 183A_U133A_Signal 183B_U133A_Signal AFFX-BioB-5_at 403.0 409.3 611.5 569.2 536.6 580.2 AFFX-BioB-M_at 757.3 574.4 826.7 595.3 755.2 956.0 AFFX-BioB-3_at 284.4 327.3 421.6 336.6 391.3 412.6 AFFX-BioC-5_at 2314.2 1685.3 2264.7 2204.1 2233.1 2458.4 AFFX-BioC-3_at 1574.5 1273.0 1484.6 1321.2 1474.7 1774.1 AFFX-BioDn-5_at 2333.7 1796.8 2464.5...

...trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_5_at ratio actin3/actinM AFFX-Dros-ACTIN_3_at AFFX-Dros-ACTIN_M_f_at ratio gapdh3/gapdh5 AFFX-Dros-GAPDH_3_at AFFX-Dros-GAPDH_5_at r...

Dear R user, I am trying to convert the contents of a date.frame to a matrix. Since there are negative values in the date.frame, when I use data.matrix(x, rownames.force = NA), the resulting matrix is not the same as the original one. Basically I think R treats the numbers in the date.frame as character and converts it to corresponding numerics. Any idea on this issue? Many Thanks, Hongyuan

...262 3.6517 0.08019 . Residuals 12 470776 39231 --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 > temp <- lapply(anovaresults, function(x) { x["Pr(>F)"][1:3,] }) > length(temp) [1] 22690 > temp[1] $"AFFX-BioB-5_at" 1 2 3 0.63906707 0.13865289 0.08018914 > gc(verbose=TRUE) Garbage collection 62 = 23+6+33 (level 2) ... 1430471 cons cells free (28%) 17.4 Mbytes of heap free (32%) used (Mb) gc trigger (Mb) Ncells 3249183 86.8 4953636 132.3 Vcells 4749443 3...

Does anyone know if it's possible to pull out the Spike-In control average intensities (BioB, BioC etc..) from a batch of un-normalised CEL files using R? [[alternative HTML version deleted]]