Using Raw .Cel Files To Make An Expression Matrix

Question

[moranr]

Hi,

Ok I did not commuinicate my previous Q correctly. I will make it more specific. Two Data series:

1 - GSE3141- I want to make this into an expression matrix.
is this correct :

gset3141 <- getGEO("GSE3141", GSEMatrix =TRUE)

?

2: GSE14814 - I want to make this into an expression matrix, but this time starting from the RAW .CEL files.
so I think my assay data can be got by using:ReadAffy() in the directory with the CEL files? my problem is getting the experimental data for this data and including it in the expression matrix?

Can someone show me code how to do this ?

Thanks for the time,

[Neilfws]

How is this different to your previous question - Making An Expression Matrix ?

[moranr]

Im focusing on a single piece of data here , not five. Im asking specifically how to get the phenotypic data into the matrix.

[moranr]

Although this q is different from the last , the sample code contained in one of the answers of my last post , does answer my question. Thanks

Answer 1

[sndrtj]

Phenotypic data is supposed to be dataframe with column 1 as CEL file names (this must be exact), and column 2 to n (as much as you'd like) as phenotypic data (e.g. disease state). Supposing you stored this in a tab delimited file (with headers), you can do:

pData(gsexxxx) <- read.table('pheno.txt',header=T,row.names=1,sep='\t')

Writing expression data to file is very easy:

write.exprs(gsexxxx.gcrma,file='file.txt')