Hi all,

Does anyone know if BitSeq can do DE on paired/matched samples?

Thanks!

Maria Jose

Hi Maria Jose,

the default BitSeq pipeline for performing DE (BitSeq stage 2) a priori assumes that the compared samples are independent, so currently it does not support possible transcript dependencies*. However, you could use the output of BitSeq stage 1 (expression estimates) to any downstream analysis which is particularly designed for this purpose (e.g: edgeR, see pg. 31 at http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf )

*PS: We do have recently incorporated a more flexible prior structure which takes into account transcript dependencies and explicitly defines a proper prior distribution for DE analysis at the transcript level. Although it is not specifically focused on the problem you mentioned, it might be worth having a look here: http://arxiv.org/abs/1412.3050

Panos