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Using Raw .Cel Files To Make An Expression Matrix

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,

r bioconductor microarray
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updated by Neilfws Neilfws • written by moranr moranr

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

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written by moranr 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

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written by moranr moranr

1 answer

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')
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written by sndrtj sndrtj

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