I can't get the probe location file from metabric

Question

[Avro]

Hi everyone,

I have the Metabric segmented data. I would like to use it the Broad Institute's GISTIC2.0 algorithm. I have everything except the markers file. The authors say they have used aroma.affymetrix package in Bioconductor and the 3 files:

• Chip definition file (GenomeWideSNP_6,Full.cdf)
• Unit fragment-length (GenomeWideSNP_6, Full,na24,HB20080214.ufl)
• Unit genome position (GenomeWideSNP_6,Full,na24,HB20080214.ugp)

How can I extract the probe locations?? I tried to download probe locations from Affymetrix but they don't match with Metabric's segmented files.

Thank you.

Answer 1

[Ar Es]

Hi Avro,

To generate a marker file you need ugp and cdf file; what you need to do is to use aroma.affymetrix package as you've already mentioned in your post.

Then create a dataframe of uniteNames of your cdf file + a dataframe from your ugp file and generate a new data frame by combining those two and use it as a marker file. It will work. I've done it for Metabric.

I hope it helped,

Arian