[aroma.affymetrix] Encountered ERROR while extracting chip effects

Hi, I was trying to perform RMA on *Mouse Exon 1.0 ST Array* as described in aroma website (link ) using custom cdf MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz

Re: [aroma.affymetrix] Encountered ERROR while extracting chip effects

doRMA() on exon arrays gives you at best exon-specific estimates (and > they are not very good estimates - FIRMA is doing a much better job on > that). > > > > On Wed, Dec 10, 2014 at 1:51 AM, Rishi Das Roy > wrote: > > Hi, > > > > I was trying to perform R

Re: [aroma.affymetrix] Custom Cdf

Hi , I have tried to do the same for MoEx10stv1 arrays by combining the BrainArray ENSE & ENSG cdfs. I have used buildCustomCdf.Public.R script from aroma website. But the resultant cdf only contains 103 units/transcript clusters. How can I built or use the BrainArray cdfs (or any other cdfs

[aroma.affymetrix] brainarray ENSG or ENST to perform FIRMA

Hi, I am trying to detect splicing events with FIRMA using brainarray ensemble CDFs ( http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v19 ) . 1) Which CDF should I use , ENSG or ENST? I have treid both for mouse. I have got 27602 and 78520 FIRMA score

[aroma.affymetrix] Re: Trouble Getting Mouse annotations after FIRMA run.

Hi Sam, I am facing similar problems to do FIRMA analysis using Mouse Exon 1.0 ST Array. Have you solved your problems. My specific questions are : 1) I was trying to use brainarray ensemble custom cdfs. There are three cdfs corresponding to it, namely ENSG, ENSE and ENST. Which one to use and