Degree of difference in transcript abundance between different pathways

[Yannick Pouliot]

Howdy. I have a user who's inquiring about the question below:

 

does the algorithm for establishing p-values for specific pathways associated with differential expression include information on the degree of difference in transcript abundance for two compared classes (eg, something analogous to a t-statistic or median fold change or...)

 

or

 

does it rely only on whether the transcript was identified as meeting some significance cutoff in a prior step (eg, all genes diff. expressed w/ a FDR of 5)?

 

Cheers and thanks,

 

Yannick

 

PS: please include the address for our user group in your response :-)

 

_______________________

Yannick Pouliot, PhD MBA

Bioresearch Informationist

Lane Medical Library &

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Information Resources and Technology

Stanford University

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