I have a set of 31 CEL files which i read into an AffyBatch object > myAB = ReadAffy() > sampleNames(myAB)  [1] "GSM2474.CEL.gz" "GSM2475.CEL.gz" "GSM2476.CEL.gz" "GSM2477.CEL.gz" "GSM2478.CEL.gz" "GSM2479.CEL.gz" "GSM2480.CEL.gz" "GSM2481.CEL.gz"  [9] "GSM2482.CEL.gz" "GSM2483.CEL.gz" "GSM2484.CEL.gz" "GSM2485.CEL.gz" "GSM2486.CEL.gz" "GSM2487.CEL.gz" "GSM2488.CEL.gz" "GSM2489.CEL.gz" [17] "GSM2490.CEL.gz" "GSM2491.CEL.gz" "GSM2492.CEL.gz" "GSM2493.CEL.gz" "GSM2494.CEL.gz" "GSM2495.CEL.gz" "GSM2496.CEL.gz" "GSM2497.CEL.gz" [25] "GSM2498.CEL.gz" "GSM2499.CEL.gz" "GSM2500.CEL.gz" "GSM2501.CEL.gz" "GSM2502.CEL.gz" "GSM2503.CEL.gz" "GSM2504.CEL.gz" I have a a CSV file containing some extra data for our samples. > disease= as.matrix(read.table("s12.csv", header=T, sep=",", row.names=1)) > rownames(disease)  [1] "968-1"  "928-1"  "934-1"  "709-1"  "930-1"  "524-1"  "455-1" "370-1"  "810-1"  "1146-1" "1161-1" "1006-1" "942-1"  "1060-1" "1255-1" "441-1" [17] "780-1"  "815-2"  "829-1"  "861-1"  "925-1"  "1008-1" "1086-1" "1105-1" "1145-1" "1327-1" "1352-1" "1379-1" "533-1"  "679-1"  "692-1" What i am trying to do is attach the extra data to the coresponding samples. Each CEL file contains this row in which its specified the pacients ID (709 in this case): ... DatHeader=[59..46191]  709  Ta gr2    ... ... Is there any way to get the sample ID list from the AffyBatch object? Thank you! [[alternative HTML version deleted]]

On Tue, Apr 27, 2010 at 2:41 AM, Popa Tiberiu <popatiberiuo at="" yahoo.com=""> wrote: > I have a set of 31 CEL files which i read into an AffyBatch object > >> myAB = ReadAffy() > >> sampleNames(myAB) > ?[1] "GSM2474.CEL.gz" "GSM2475.CEL.gz" "GSM2476.CEL.gz" "GSM2477.CEL.gz" "GSM2478.CEL.gz" "GSM2479.CEL.gz" "GSM2480.CEL.gz" "GSM2481.CEL.gz" > ?[9] "GSM2482.CEL.gz" "GSM2483.CEL.gz" "GSM2484.CEL.gz" "GSM2485.CEL.gz" "GSM2486.CEL.gz" "GSM2487.CEL.gz" "GSM2488.CEL.gz" "GSM2489.CEL.gz" > [17] "GSM2490.CEL.gz" "GSM2491.CEL.gz" "GSM2492.CEL.gz" "GSM2493.CEL.gz" "GSM2494.CEL.gz" "GSM2495.CEL.gz" "GSM2496.CEL.gz" "GSM2497.CEL.gz" > [25] "GSM2498.CEL.gz" "GSM2499.CEL.gz" "GSM2500.CEL.gz" "GSM2501.CEL.gz" "GSM2502.CEL.gz" "GSM2503.CEL.gz" "GSM2504.CEL.gz" > > I have a a CSV file containing some extra data for our samples. > >> disease= as.matrix(read.table("s12.csv", header=T, sep=",", row.names=1)) >> rownames(disease) > ?[1] "968-1"? "928-1"? "934-1"? "709-1"? "930-1"? "524-1"? "455-1"? "370-1"? "810-1"? "1146-1" "1161-1" "1006-1" "942-1"? "1060-1" "1255-1" "441-1" > [17] "780-1"? "815-2"? "829-1"? "861-1"? "925-1"? "1008-1" "1086-1" "1105-1" "1145-1" "1327-1" "1352-1" "1379-1" "533-1"? "679-1"? "692-1" > > What i am trying to do is attach the extra data to the coresponding samples. > > Each CEL file contains this row in which its specified the pacients ID (709 in this case): > > ... > DatHeader=[59..46191]? 709? Ta gr2??? ... > ... > > Is there any way to get the sample ID list from the AffyBatch object? Not a direct answer, but since these data are from NCBI GEO, why not use GEOquery to get the information about samples? library(GEOquery) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RCurl Loading required package: bitops > gse <- getGEO('GSE88')[[1]] Found 1 file(s) GSE88_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE88/GSE 88_series_matrix.txt.gz' ftp data connection made, file length 492380 bytes opened URL ================================================== downloaded 480 Kb File stored at: /var/folders/F+/F+PwkbXqF6WeunvinD8pZk+++TI/-Tmp-//Rtmp2M4lZS/GPL80.so ft > head(pData(gse)) title geo_accession status GSM2474 Bladder sample 709-1 GSM2474 Public on Dec 08 2002 GSM2475 Bladder sample 928-1 GSM2475 Public on Dec 08 2002 GSM2476 Bladder sample 930-1 GSM2476 Public on Dec 08 2002 GSM2477 Bladder tumour 934-1 GSM2477 Public on Dec 08 2002 GSM2478 Bladder sample 968-1 GSM2478 Public on Dec 08 2002 GSM2479 Bladder sample 1006-1 GSM2479 Public on Dec 08 2002 > sessionInfo() R version 2.11.0 Under development (unstable) (2009-11-13 r50424) i386-apple-darwin10.2.0 locale: [1] en_US/en_US/C/C/en_US/en_US attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GEOquery_2.11.2 RCurl_1.3-1 bitops_1.0-4.1 Biobase_2.7.3