CBS only on CN data instead of using both CN and SNP data

[yu song]

Hi aroma group,

 I am wondering could we only do CBS on the CN data without SNP in it. 

In the affymetrix6  the input(raw data) contains both CN and

 SNP. How could I get the CBS result only with CN?

 Thanks.

 Best regards,

 Yu Song

[Henrik Bengtsson]

Hi,

there is no direct way to segment only non-polymorphic loci ("CN
probes")/exclude SNPs, but one approach would be to create a custom
UGP annotation data file where the genomic positions for all SNPs as
set to missing (=NA), and then explicitly use that UGP file when
segmenting the data.

/Henrik

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