[BioC] justRMA using incorrect default cdf

[Kimpel, Mark William]

Jim,

The problem appears to be a corrupt data file as I cannot reproduce the
error with other datasets.

To answer your other questions... I put the eset into a list with
another slot reserved for annotation information. That way I only have
to build the annotation once and then store it in a database with the
eset. Maybe a bit odd, but I'm not a trained programmer and it works for
me.

The read.pData.ordered.func function is something I wrote to make sure
that the proper phenotype information was correctly assigned to samples.
Not long ago I needed to sort my pdata file by phenotype to check
something and forgot to resort it by sampleName before saving it. After
getting some puzzling analysis results I discovered that read.phenoData
does not match sampleNames with CEL file names (in my case one and the
same) so I wrote this function to do that. I will share the code, simple
as it is, in case this is beneficial to anyone else (see below).

Thanks,

Mark


read.pData.ordered.func<-function(pdata.file)

{

pD <- read.phenoData(filename = pdata.file, sep = "\t", header=TRUE,
row.names=1)

cel.files<-list.celfiles()

for (i in 1:length(cel.files))

    {
    
    cel.files[i]<-substr(x=cel.files[i], start=1,
stop=(nchar(cel.files[i])-4))
    
    
    }

pos<-match(cel.files, rownames(pD at pData))

pD<-pD[pos]

pD


}