Question: Whole Blood Gene Expression Deconvolution
1
gravatar for michaelsbreen1
5.0 years ago by
University of Southampton
michaelsbreen160 wrote:

Hi all,

We routinely work with gene-expression data sets generated from whole-blood of subjects of case and control status. Recently, there seems to be quite an interest in deconvolving cell-type specific gene-expression signatures from whole blood and we too think this is an interesting concept.

Numerous programs available: CellMix csSAM DeMiX iSOLATE PERT DeconSeq (for RNA-Seq) and I am sure there are others...

I have three main questions:

  1. For now we are interested in exploring the utility of CellMix and csSAM. I am under the impression that CellMix can deconvolve cell-type signatures from whole-blood with out any prior knowledge of cell-type frequencies where csSAM deconvolves known cell-types signatures (and measures strength of differential expression between cell-tyes). Is this a correct assessment?

  2. Described usage of these programs is slightly ambiguous. Can someone point me towards towards working example (as in a proper usage guid) of deconvolving cell-type contributions to whole blood gene-expression of samples with unknown cell-types using CellMix and csSAM? I find the below links very vague descriptions of how to perform this on local data-sets. In other words, starting with a gene-expression matrix derived from whole-blood and estimating cell-type proportions and using csSAM to perform differential expression on these cell-types across two conditions. Any help is much appreciated.

  3. For this specific case, do we think that an analysis using first CellMix to deconvolve whole-blood cell-types following by csSAM to be an effective pipeline?

CellMix: http://web.cbio.uct.ac.za/~renaud/CRAN/web/CellMix/blood.html csSAM: http://cran.r-project.org/web/packages/csSAM/csSAM.pdf

Yours, Michael

expression • 3.2k views
ADD COMMENTlink written 5.0 years ago by michaelsbreen160

Did you have success in running CellMix or csSAM? Are you working on microarray or RNA-seq data?

ADD REPLYlink written 4.4 years ago by Christian2.8k

Hi Michael, Have you had any headway into this? I am working on CellMix Currently and would really need some help with this.

Thanks,Venkat

ADD REPLYlink written 3.1 years ago by gemini.venkat0
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