Hi, This seems to be working well, although I'm concerned with the raw counts > distributions of some cell lines as they look skewed to negative values > (histogram attached, apologises for the poor quality). > > Actually, I have seen this effect also using as reference the average of a > batch (~250 samples) of SNP6 normal samples. My end goal is to obtain > GISTIC scores and when I fed the CbsModel output to GISTIC I noticed that > there are more '-1's than '0's, again showing there is a skew to negative > ratios. > > Am I missing any preprocessing that is required besides the doCRMAv2? >
Just to follow up, if I follow the vignette CRMAv2 with all the steps (http://aroma-project.org/vignettes/CRMAv2/) the histogram of the ratios is now centred on zero, attached. Is doing step-by-step slower than 'doCRMAv2'? It seemed to be taking more time, but I haven't calculated the differences. In the vignette code: if (length(findUnitsTodo(plm1)) > 0) { # Fit CN probes quickly (~5-10s/array + some overhead) units1 <- fitCnProbes(plm1, verbose=verbose) str(units1) # int [1:945826] 935590 935591 935592 935593 935594 935595 ... # Fit remaining units, i.e. SNPs (~5-10min/array) units1 <- fit(plm1, verbose=verbose) str(units1) } Is not processing the SNPs an option if you are only interested in copy-number changes? That would be ideal :) Thanks, -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
