[BioC] question about how analysis affymetrix huex st array

cstrato cstrato at aon.at
Wed May 23 19:45:05 CEST 2012

Dear Jianhong,

You do not describe what you are comparing:

You say that you tried oligo, xps, aroma.affymetrix, and also 
APT(Affymetrix Power Tools). Then you say that only the results of MiDAS 
from APT and results of FIRMA from aroma.affymetrix have about 40% 
overlap. All the others have less than 10% overlap.
What do you mean with less than 10% overlap???
What did you compare???

Please note that MIDAS was developed by Affymetrix as alternative to 
ANOVA to measure differences between exon level signal...
The Affymetrix "exon_alt_transcript_analysis_whitepaper.pdf" says:
The basic idea is the following:
• We use PLIER to generate a robust estimate...

It seems that you are comparing apples and oranges, since you seem to 
compare MIDAS (based on PLIER) to RMA!?

If you want to compare the different packages you need to compare the 
results obtained from e.g. RMA and not from MIDAS, which most packages 
did not implement (although xps has implemented FIRMA).

With respect to APT vs xps please read the vignette "APTvsXPS.pdf" where 
the reasons for the slight differences between the RMA results obtained 
with APT or xps are explained.

C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

On 5/23/12 2:55 AM, Ou, Jianhong wrote:
> Dear lists,
> I am doing some analysis of HuEx-1_0-st-v2 chip. I tried R package oligo, xps, aroma.affymetrix. I also tried Affymetrix power tools, JETTA and Atlanalyze. After that I feel very confused about my results. Only the results of MiDAS from APT and results of FIRMA from aroma.affymetrix have about 40% overlap. All the others less than 10% overlap. Is that normal?
> The code for MiDAS is from paper: Exon array data analysis using Affymetrix power tools and R statistical software, Helen E. Lockstone, Brief Bioinform (2011), doi: 10.1093/bib/bbq086
> The code for FIRMA is from webpage: http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis, and followed with log2 transform and do analysis with LIMMA.
> The code for JETTA is from webpage: http://gluegrant1.stanford.edu/~junhee/JETTA/instructions.html#rex
> All the parameters are followed the sample codes.
> Please, help me.
> Yours sincerely,
> Jianhong Ou
> jianhong.ou at umassmed.edu<mailto:jianhong.ou at umassmed.edu>
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