Question: Using Raw .Cel Files To Make An Expression Matrix
2
gravatar for moranr
6.4 years ago by
moranr250
Ireland
moranr250 wrote:

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 • 3.8k views
ADD COMMENTlink modified 6.3 years ago by Neilfws48k • written 6.4 years ago by moranr250

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

ADD REPLYlink written 6.4 years ago by Neilfws48k

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

ADD REPLYlink written 6.3 years ago by moranr250

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

ADD REPLYlink written 6.3 years ago by moranr250
4
gravatar for sndrtj
6.4 years ago by
sndrtj180
Netherlands
sndrtj180 wrote:

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')
ADD COMMENTlink written 6.4 years ago by sndrtj180
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