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wwylab / DeMixT

GNU General Public License v3.0
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Is it possible to extract tumor-only gene expression profile for whole transcriptome? #13

Closed lxhuang7 closed 3 years ago

lxhuang7 commented 3 years ago

Hi, Thanks for this wonderful tool. I'm trying to switch from ISOpure to DeMixT. One question though, can I extract tumor-only expression matrix for all genes in my admixed RNA-seq data by just setting if.filter = FALSE? Do I need to change other parameters accordingly? It is not very clear to me in the vignette. Thanks again!

ShaolongCao commented 3 years ago

"if.filter = FALSE" will force DeMixT algorithm to use all available genes to fit the deconvolution model, which is not recommended. We suggest to use "if.filter = TRUE" option, which will improve tumor proportion estimation. Currently, we have a built-in filter in the function DeMixT_S2 to filter out unidentifiable genes in terms of the deconvolved expression (tumor-only expression). Consequently, it is likely that some genes will be dropped since the deconvolved expression value will be unreliable.

lxhuang7 commented 3 years ago

Thank you very much for the explanation.

guodudou commented 2 years ago

@lxhuang7 Hello! Sorry for bothering you. I am trying to identity a tool for tumor profile deconvolution and have ISOpure and DeMixT. I am curious what are the reasons for you to switch from ISOpure to DeMixT? Thanks!