[aroma.affymetrix] extract LRR and BAF from ACNE results

Dear Aroma.affymetrix teem, I followed the vignette "Allele-specific copy numbers using non-negative matrix factorization". I want to extract LRR and BAF to feed into another software "ASCAT " to correct aneuploidy and normal contamination. >From

[aroma.affymetrix] cfit error while doCRMAv2

Hi, I am following the vignette on paired total copy number analysis. So far, my cdf files and the rawData directory structure looks ok. When I do dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose) I get the following error and I can't see a dsList object created. Er

Re: [aroma.affymetrix] cfit error while doCRMAv2

First of all, what versions of packages do you have, e.g. what's the output sessionInfo() after doing: library("aroma.affymetrix") library("sfit") sessionInfo() /Henrik On Fri, May 29, 2015 at 9:51 AM, arshi wrote: > Hi, I am following the vignette on paired total copy number analysis. > > So

Re: [aroma.affymetrix] extract LRR and BAF from ACNE results

So, there are few things here: 1. In the Aroma Framework, we always try to store estimates/signals on the "original" scale, e.g. even if, say, chip-effect estimates are original on the log scale, we unlog those before saving. That is a policy with the rationale that all data can always be represe

Re: [aroma.affymetrix] cfit error while doCRMAv2

Sorry about not posting that. > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.2 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSA

Re: [aroma.affymetrix] cfit error while doCRMAv2

This all looks good, so it's indeed a weird error that I most likely think is due to some hiccups when the 'sfit' package was installed (which defines the cfit() function). For troubleshooting, first try: url <- "https://raw.githubusercontent.com/HenrikBengtsson/aroma.core/develop/tests/fitGenot

Re: [aroma.affymetrix] cfit error while doCRMAv2

BTW, the output of packageDescription("sfit") is also useful for troubleshooting - it will particularly tell you when and for what version of R it was build and installed. /Henrik On Fri, May 29, 2015 at 4:33 PM, Henrik Bengtsson wrote: > This all looks good, so it's indeed a weird error tha