Re: [aroma.affymetrix] mufColumns on genes with more than 500 probes across the gene

Hi Iain, Can you send me a reproducible example, plus the output of sessionInfo() and traceback() after the error, please? It'll probably be too large for email, so maybe use Dropbox or dropsend .. My guess is that the units with >500 probes actually have NAs. Maybe you can check this also b

[aroma.affymetrix] HuEx-1_0-st-v2 gcRMA

Hello, I am having trouble getting gcRMA to work with a human exon array. I know this has been addressed before, eg: https://groups.google.com/forum/#!msg/aroma-affymetrix/QD6o-3XiifM/e8-5OaQ44qgJ, but my issue is slightly different. I used the code presented in that thread but got the follow

Re: [aroma.affymetrix] Changing the Aroma settings (RMA MedianPolish threshold ) in the latest version of the aroma.affymetrix

Hi, could you please share the exact calls you are using and elaborate a bit more what makes you think it's not working? That'll help me help you. Henrik On Thu, Jun 4, 2015 at 6:40 AM, sanjana wrote: > Hi, > > Our group is working with HTA platform and using aroma.affymetrix for the > analys

[aroma.affymetrix] mufColumns on genes with more than 500 probes across the gene

Hi We're trying to calculate the difference in residuals between two groups and generate mufScores (FIRMAGene) on those residual differences. Calculating the differences goes smoothly: rsu_diff <- lapply(unlist(rsu, use.names=FALSE), byrow=FALSE, ncol=length(unique(cls))) where cls is a group

[aroma.affymetrix] Changing the Aroma settings (RMA MedianPolish threshold ) in the latest version of the aroma.affymetrix

Hi, Our group is working with HTA platform and using aroma.affymetrix for the analysis. We intend to change the RMA median polish threshold in aroma settings. We are able to achieve this in version 2.13.1 but somehow not in version 2.13.2? Has anyone else experienced the same thing? Is it p