[BioC] continued problems with ReadAffy

[Kimpel, Mark William]

After thinking that I had the problem solved, I am continuing to have
problems with "ReadAffy". The default options of the function are still
leading to the error " sampleNames different from names of phenoData
rows" and I am unable to figure out its cause. See below for output and
sessionInfo(). It appears to me that the samplenames and rownames of
phenodata are identical and I have used setdiff() to verify this (output
is character(0) ).

Ideas?  Thanks, Mark

> ReadAffy()
Error in validObject(.Object) : invalid class "AffyBatch" object:
sampleNames different from names of phenoData rows

Enter a frame number, or 0 to exit   

1: ReadAffy()
2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData,
description = l$description, notes = notes, compress = compress, r
3: new("AffyBatch", exprs = .Call("read_abatch", filenames, compress,
rm.mask, rm.outliers, rm.extra, ref.cdfName, dim.intensity, verb
4: initialize(value, ...)
5: initialize(value, ...)
6: validObject(.Object)

Selection: 2
Called from: eval(expr, envir, enclos)
Browse[1]> ls()
 [1] "auxnames"      "cdfname"       "compress"      "description"
"dim.intensity" "filenames"     "headdetails"  
 [8] "n"             "notes"         "pdata"         "phenoData"
"ref.cdfName"   "rm.extra"      "rm.mask"      
[15] "rm.outliers"   "samplenames"   "sd"            "verbose"      
Browse[1]> samplenames
 [1] "BB01R018.CEL" "BB01R019.CEL" "BB01R020.CEL" "BB01R021.CEL"
"BB01R022.CEL" "BB01R023.CEL" "BB01R024.CEL" "BB01R025.CEL"
 [9] "BB01R026.CEL" "BB01R027.CEL" "BB01R029.CEL" "BB01R030.CEL"
"BB01R031.CEL" "BB01R032.CEL" "BB01R033.CEL" "BB01R034.CEL"
Browse[1]> pdata
             sample
BB01R018.CEL      1
BB01R019.CEL      2
BB01R020.CEL      3
BB01R021.CEL      4
BB01R022.CEL      5
BB01R023.CEL      6
BB01R024.CEL      7
BB01R025.CEL      8
BB01R026.CEL      9
BB01R027.CEL     10
BB01R029.CEL     11
BB01R030.CEL     12
BB01R031.CEL     13
BB01R032.CEL     14
BB01R033.CEL     15
BB01R034.CEL     16
Browse[1]> c

Enter a frame number, or 0 to exit   

1: ReadAffy()
2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData,
description = l$description, notes = notes, compress = compress, r
3: new("AffyBatch", exprs = .Call("read_abatch", filenames, compress,
rm.mask, rm.outliers, rm.extra, ref.cdfName, dim.intensity, verb
4: initialize(value, ...)
5: initialize(value, ...)
6: validObject(.Object)

Selection: 0
> sessionInfo()
Version 2.3.0 Under development (unstable) (2006-01-01 r36947) 
i386-pc-mingw32 

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
"datasets"  "base"     

other attached packages:
   affy Biobase RWinEdt 
"1.9.7" "1.9.6" "1.7-4"

Mark W. Kimpel MD 

 

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Department of Psychiatry

Indiana University School of Medicine

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