[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

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

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

Edit: Never mind. I had missed the calls to: computeAffinities(cdfS, verbose=-8) getAromaCellSequenceFile(cdfS) so, after downloading the ACS file and running the above line, now gcRMA appears to be working fine. # updated code sequence ## library('aroma.affymetrix')

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

On Fri, Jun 5, 2015 at 8:09 AM, sanj sood.sanj...@gmail.com wrote: Hi Henrik, Thanks for replying. We are not completely sure if its the issue with the version of aroma.affymetrix or not. We were trying to use the function mufColumn from FIRMAGene library on HTA platform with Brain array

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

Hi Henrik, Thanks for replying. We are not completely sure if its the issue with the version of aroma.affymetrix or not. We were trying to use the function *mufColumn* from FIRMAGene library on *HTA* platform with *Brain array gene level cdf. *However it didn't work and we got the following