How To Create Tab-Delimited Copy Number Files From Aroma.Affymetrix Output

Question

[Jason]

Hi,

I have checked the whole aroma.affymetrix website but I can't seem to work out their tutorials on creating a tab-delimited text file from doCRMAv2() output.

What I need is a table with following columns

Each sample contains the LogR. Any help would be a appreciated!!

Thanks Jason

[Irsan]

What is your design ? Case -Control, case - median of all cases, case - pool of external references? BTW, there is lots of documentation about this on the aroma affymetrix website

[Jason]

Case-median of all cases. I went through the website the whole day and somehow always ended up on the "Write a tab-delimited UGP" an related link which give incomplete information on the problem. Somehow, this page never showed up. One of those days I guess. Thanks a lot, I will try this too.

[Jason]

I checked the link you shared and that's only for writing raw values from dataset whereas I'm interested in writing the ouput of doCRMAv2 into a tab-delim file as above.

Answer 1

[Irsan]

dsList <- doCRMAv2(...)
dsAll <- dsList$total
dfR <- getAverageFile(dsAll)
cn.estimates <- exportTotalCnRatioSet(dsAll, ref=dfR)

[Jason]

Thanks a lot. Could you also tell how to use doCRMAv2 using a additional .CEL files/dataset as reference? I have checked its help file and I can't find a way to add external dataset as reference.

[Irsan]

You mean how to compare your own samples compared to a baseline/pooled reference of external samples?