On Thu, Dec 23, 2010 at 2:08 PM, allab <asphod...@googlemail.com> wrote: > Dear aroma users/authors, > i am doing now Affy 6.0 SNP data analysis. > I have generated fracB values with aroma package and see now that > there are also NA values present. What could be the reason for this > and with what values could i replace them meaningfully?
The Affymetrix GenomeWideSNP_6 chip type contains ~900,000 SNPs and ~900,000 non-polymorphic loci, cf. http://aroma-project.org/chipTypes/GenomeWideSNP_6 Allele B fractions (BAFs) are only defined for SNPs. For the non-polymorphic loci, the BAFs are reported as missing values (NAs). /Henrik > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
