Search
Question: Expression deconvolution using PSEA: applicable to RNA-seq?
1
gravatar for WouterDeCoster
4 months ago by
Antwerp, Belgium
WouterDeCoster110 wrote:

I came across the PSEA package which is used for computational deconvolution of microarray expression datasets. Their paper demonstrates its usage on human brain microarray data.

The paper and reference manual mention microarray, but I wonder if the same method is applicable to RNA-seq data? Considering the model is different, I'd initially suspect it isn't. But does someone know an alternative? The majority of the deconvolution methods I've seen are optimized/tested for impure tumors, which may or may not a representative system for the complexity in celltype composition in the case of neurodegeneration.

Thanks in advance!

ADD COMMENTlink written 4 months ago by WouterDeCoster110

I'd love an answer to this too. I have found CIBERSORT (https://www.nature.com/articles/nmeth.3337) which gives estimation of cell types, and is flexible to type of sample if you can find expression data from "pure cell" populations, but does not estimate expression level per cell type

ADD REPLYlink written 3 months ago by daigle72090
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 119 users visited in the last hour