Variation Callings From Nextgen Genome Sequence Into Gene Expression

Question

[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

Answer 1

[Michael]

Have a look at the pdInfoBuilder package in Bioconductor to build your own annotations. But before you mess around with the array descriptions I would rethink the concept of increasing statistical power by removing probes. I think this is not the case and you are misinterpreting the article you cite. The article is from 2005, you might fare better with using the most up-to-date array annotations.