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@umassmed.edu<mailto:jianhong.ou@umassmed.edu>



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