Question

Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis

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Bernardo ▴ 10

@27b596fa

Last seen 19 months ago

United States

Hello,

I am doing a pilot study using bulk RNAseq data for differential expression in human brain tissue from healthy controls and Alzheimer's patients. I performed a cell type deconvolution analysis to determine if the control samples and Alzheimer's samples have a different proportion of neuronal vs non-neuronal cells. The Alzheimer's tissue shows a consistent trend of having ~10% less neuronal cells.

I know it would be possible to add a continuous covariate such as percent neuronal cells to the DESeq2 differential expression analysis, but I was wondering if this approach seems sound? Would it be better to add a covariate for percent neuronal cells or try to do some kind of normalization using genes only expressed in neurons?

This is a pilot to a much larger study we are planning on doing and I am trying to make sure the differential expression we find is not due to neuronal death associated with Alzheimer's.

Any input will be much appreciated!

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DESeq2 Dese DifferentialRegulation differe • 1.7k views

ADD COMMENT • link updated 6 months ago by ij283 • 0 • written 20 months ago by Bernardo ▴ 10

score 3 · Accepted Answer · 2023-04-12

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Michael Love 43k

@mikelove

Last seen 1 day ago

United States

I have used composition as a control factor before. It's better to add covariates than to try to manipulate the counts.

There are methods like BMIND that attempt to do DE on the CTS expression (inferred). Worth looking into.

ADD COMMENT • link 20 months ago Michael Love 43k

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Hi Michael,

I'm sorry to bother you, but I still have some questions about your comment.

The main question is what is "control factor"? And could you please tell me what did you do with "control factor"? Is it normalize? Could you please tell me more detail?

Thanks!

ADD REPLY • link 9 months ago feather-W • 0

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See the vignette. I refer to adding a factor to the design. We have batch in the quick start section.

ADD REPLY • link 9 months ago Michael Love 43k

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Ok, thanks for your help!

ADD REPLY • link 9 months ago feather-W • 0

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I have the exact same query but with different types of cells. Hence, my question is : would it be possible to add another cell type proportion instead of one into the batch listed below as follow

Batch <- neuronal cells + glial cells

 dds <-DESeqDataSetFromMatrix(countData = cts,
                              colData = coldata,
                              design= ~ batch + condition)

Many thanks in advance

ADD REPLY • link 6 months ago ij283 • 0