[BioC] ReadAffy question

[James W. MacDonald]

Kimpel, Mark William wrote:
> I work with CEL files that frequently have names assigned randomly in
> respect to phenotype. I create my pdata files by modifying spreadsheets
> with file and phenotype information already in appropriate columns. I
> had been assuming that it did not matter what order the filenames were
> in in the first column of the pdata file, that after being read in the
> CEL files would be matched to the appropriate row in pdata and would
> thus have the correct phenotype assigned.
> 
> Some recent work has indicated to me that this is probably NOT the case,
> instead, it appears that the files are read in by filename alphanumeric
> order and the phenotype and sample is assigned by row order of the pdata
> file. This, of course, will often result in incorrect sample names and
> phenotypes being assigned to files.
> 
> I have searched the documentation and help files for an answer to this
> question to no avail.
> 
> How is this supposed to work?

Two ways; you can either input your data using the widget-based 
interface, or the way you are doing things now except with the rows of 
the phenoData object in alphanumeric order. The function read.affybatch 
simply takes the phenoData object as is, and assumes you have ordered 
things correctly.

The relevant line in read.affybatch() is this:

samplenames <- rownames(pdata)

A call to list.celfiles() can be used to set the order of your phenoData 
object to ensure things line up correctly.

Best,

Jim


> 
> SessionInfo()
> 
> Version 2.3.0 Under development (unstable) (2006-01-01 r36947) 
> i386-pc-mingw32 
> 
> attached base packages:
>  [1] "tcltk"     "splines"   "tools"     "methods"   "stats"
> "graphics" 
>  [7] "grDevices" "utils"     "datasets"  "base"     
> 
> other attached packages:
>     tkWidgets        DynDoc    reposTools   widgetTools    rat2302cdf 
>       "1.9.0"       "1.9.0"       "1.9.1"       "1.7.0"       "1.5.1" 
> affycoretools       GOstats      multtest    genefilter      survival 
>       "1.3.1"       "1.5.4"       "1.8.0"       "1.9.2"        "2.20" 
>        xtable          RBGL      annotate            GO         graph 
>       "1.3-0"       "1.7.6"       "1.8.0"       "1.6.5"       "1.9.4" 
>         Ruuid       cluster         limma          affy       Biobase 
>       "1.9.0"      "1.10.2"       "2.4.4"       "1.9.6"       "1.9.2" 
>       RWinEdt 
>       "1.7-3"
> 
> 
> Mark W. Kimpel
> I.U. School of Medicine
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623