Question: Deconvolution methods on RNAseq data
1
gravatar for Ron
5 months ago by
Ron600
United States
Ron600 wrote:

Hi all,

This question is similar to this post. C: Deconvolution Methods on RNA-Seq Data (Mixed cell types)

I have been using CIBERSORT and DeconRNAseq, but both of them give different results.

  1. Does anyone know of other cell type signatures besides LM22 from CIBERSORT which has only 22 cell types? Signatures that could include fibroblasts etc besides the 22 cells provided in LM22.

  2. Also,are there any other tools for RNAseq besides CIBERSORT and DeconRNAseq?

  3. Are there any softwares which consider other factors into account such as tumor purity before doing deconvolution?

Thanks,

Ron

ADD COMMENTlink modified 4 months ago by shauty0 • written 5 months ago by Ron600
1

NB that the authors of CIBERSORT warn against using it on RNAseq (from their webpage):

LM22 was designed and validated on gene expression microarray data, specifically on the following platforms: Affy U133A/Plus2 and Illumina Expression BeadChip (HumanHT-12 v4). Users wishing to apply LM22 to other array platforms (e.g. Agilent single or two-color) or to RNA-Seq data should be forewarned that LM22 has not been validated for these platforms, and the results may not be reliable.

We are in the process of deriving an immune subset signature matrix for RNA-Seq and will inform registered users when it becomes available.

ADD REPLYlink written 4 months ago by bruce.moran240

Are you still working on getting LM22 signature?

ADD REPLYlink written 3 months ago by Ron600

This is a quote from the CIBERSORT webpage, so I am not generating an RNAseq-based LM22 signature myself, no.

ADD REPLYlink written 12 weeks ago by bruce.moran240
0
gravatar for shauty
4 months ago by
shauty0
shauty0 wrote:

Hi, I just stumbled across this http://xcell.ucsf.edu/ . What's your experience with CIBERSROT? When I tried CIBERSORT I got only 16 results with p-value<0.05 from 75 cancer RNA seq samples.

ADD COMMENTlink written 4 months ago by shauty0
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