Hi everyone, I successfully applied CRMAv2 for estimating copy numbers from a set of 14 paired samples, and after the segmentation process I used chromosome explorer for displaying the results. The problem is that the regions positions listed in regions.xls file are all shifted forward 13 nucleotides, compared to the genomic locations of the probes provided by Affymetrix (i checked only CN probes....but also SNPs probes are shifted forward some nucleotide..). Does anyone knows how to solve this ?
I created new UGP, UFL and ACS files following this guides: - for UGP: http://www.aroma-project.org/node/43 (importing from NetAffx files) and using the newest affymetrix files: GenomeWideSNP_6.na32.annot.csv, GenomeWideSNP_6.cn.na32.annot.csv.zip; - for UFL: http://www.aroma-project.org/node/47 (importing from NetAffx files) and using the newest affymetrix files: GenomeWideSNP_6.na32.annot.csv, GenomeWideSNP_6.cn.na32.annot.csv.zip; - for ACS: http://www.aroma-project.org/node/100 (importing from Affymetrix probe-tab file) and using the affymetrix files: GenomeWideSNP_6.CN_probe_tab and GenomeWideSNP_6.probe_tab. - CDF file: i downloaded the library file genomewidesnp6_libraryfile from affymetrix website and extracted the GenomeWideSNP_6.cdf file For segmentation I used both CBS and GLAD, but the issue remain. Could someone help me ? Thank you very much, Cristian -- 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
