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Danko-Lab / TED

a fully Bayesian approach to deconvolve tumor microenvironment
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Also output tumor expression profile #4

Closed kvittingseerup closed 4 years ago

kvittingseerup commented 4 years ago

Hi Tinyi

Would it be possible to also output the "pure" tumor expression profiles estimated by TED? Just like we can now get the "pure" stromal expression profiles from ted_resut$res$phi.env.

Cheers Kristoffer

tinyi commented 4 years ago

There are a few versions of tumor expression provided by TED listed as below. You may also refer to the vignette for details.

tcga.ted$res$first.gibbs.res$ Znkg # the mean of posterior reads in each cell type of each bulk sample

tcga.ted$res$ Zkg.tum.norm # the depth-normalized count of tumor expression in each bulk sample (the zero count genes adjusted to the same small value for each sample)

tcga.ted$res$ Zkg.tum.vst # the variance stabilizing transformed count of tumor expression in each bulk sample (by the vst function in DESeq2)

On Wed, Feb 12, 2020 at 4:59 AM Kristoffer Vitting-Seerup < notifications@github.com> wrote:

Hi Tinyi

Would it be possible to also output the "pure" tumor expression profiles estimated by TED? Just like we can now get the "pure" stromal expression profiles ted_resut$res$phi.env.

Cheers Kristoffer

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kvittingseerup commented 4 years ago

Hi Tinyi

That is simply me being to fast. Thanks :-)