Variation callings from NextGen genome sequence into gene expression

[houkto]

Hi there,

I am trying to find a script or a tools that removed the probes in a cdf file of a expression data using the variant discovery from comparing two strains? so we can improved our statistical power. we will also be using the custom cdf ("Evolving Gene/Transcript Definitions Significantly Alter the Interpretation of GeneChip Data" Nucleic Acid Research 33 (20), e175) which will also will have an effect to improve the detection of finding differential expression genes.

thanks in advance