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I can't get the probe location file from metabric

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.

metabric gistic cdf
• 2,590 views • link
updated by Ram Ram • written by Avro Avro

1 answer

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

• 0 views • link
updated by Ram Ram • written by Ar Es • Ar Es

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