[aroma.affymetrix] Estimating tumor purity from affymetrix snp6.0 copy nrs

Dear Henrik, I know my posting is not related to aroma.affymetrix, but I couldn't find anyone but you that I can ask about this issue. I am very sorry for the inconvenience I might have caused. I urgently need to get tumor purity estimate for copy nrs from matched tumor-normal pairs on the

[aroma.affymetrix] accessing chip effect sets

Dear all, After processing Affymetrix GenomeWide SNP 6.0, I wanted to access 'chip effect data set' by using: cesN - CnChipEffectSet$byName(AffyTestData,tags=ACC,ra,-XY,BPN,- XY,AVG,FLN,-XY, chipType=GenomeWideSNP_6) But, it failed, generating an error message: can't locate... Using the

[aroma.affymetrix] An error message from running PSCBS

Dear Henrik, I have been doing paired PSCBS analysis on a Genome Wide SNP array 6.0 data set in order to estimate LOH for 20 pairs of samples. The code on the aroma web site successfully estimated LOH for most pairs, while it fails to estimate LOH for several bad pairs. An error message I got from