Hello, all; searched but did not find a solution to this. I have some 6.0 arrays that I've normalized and done calls for with as per the oligo vignette. However, the calls are still in the 1/2/3 format and I'd like to get them into (preferably) an IUPAC code for the actual forward strand nucleotide. Is there an easy way to do this? Hollis Wright, PhD Knight Cancer Center Oregon Health and Science University

Dear Hollis, if your dataset is comprised of samples on the SNP 6.0 chip, I'd strongly recommend you to use the 'crlmm' package to get the genotype calls. The algorithm in that package has the improvements described in [1]. However, it'll still give you calls in the 1/2/3 format. Currently, there are no tools to give you calls in the IUPAC code. You could do this 'manually' by comparing the results you get against a table having the SNP ID, allele A, allele B and strand info, which you can obtain with: library(pd.genomewidesnp.6) conn = db(pd.genomewidesnp.6) sql = 'SELECT man_fsetid, allele_a, allele_b, strand FROM featureSet' snpInfo = dbGetQuery(conn, sql) On the 'snpInfo' table, please note that 0 stands for sense and 1 stands for antisense strand. HTH, benilton [1] Carvalho BS, Louis TA, Irizarry RA. Quantifying uncertainty in genotype calls. Bioinformatics. 2010 Jan 15;26(2):242-9. Epub 2009 Nov 11. PMID: 19906825 On 25 April 2011 21:34, Hollis Wright <wrighth at="" ohsu.edu=""> wrote: > Hello, all; searched but did not find a solution to this. I have some 6.0 arrays that I've normalized and done calls for with as per the oligo vignette. However, the calls are still in the 1/2/3 format and I'd like to get them into (preferably) an IUPAC code for the actual forward strand nucleotide. Is there an easy way to do this? > > Hollis Wright, PhD > Knight Cancer Center > Oregon Health and Science University > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)