This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How To Create Tab-Delimited Copy Number Files From Aroma.Affymetrix Output

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 enter image description here

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

Thanks Jason

r affymetrix
• 3,973 views • link
updated by Irsan Irsan • written by Jason • Jason

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

• 375 views • link
written by Irsan Irsan

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.

• 0 views • link
written by Jason • 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.

• 0 views • link
written by Jason • Jason

1 answer 

dsList <- doCRMAv2(...)
dsAll <- dsList$total
dfR <- getAverageFile(dsAll)
cn.estimates <- exportTotalCnRatioSet(dsAll, ref=dfR)
• 128 views • link
written by Irsan Irsan

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.

• 0 views • link
written by Jason • Jason

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

• 0 views • link
written by Irsan Irsan

Log in to answer this question.

More posts like this