Question: Representative gene expression value in one condition with several replicates
0
16 months ago by
Jack0
Jack0 wrote:

Hi all,

I want to know how to get a gene expression value for a condition with different replicates.

For example, I have condition M and N, each condition with two replicates M1, M2, N1, N2

I want to get one value to represent the gene expression value (FPKM or TPM) of M, can I just use the mean of each replicate? M=(M1+M2)/2?

Is there any other way to calculate the gene expression value for a condition?

rnaseq edger gene expression • 559 views
modified 16 months ago by Gordon Smyth37k • written 16 months ago by Jack0
Answer: Representvie gene expression value in one condition with several replicates
5
16 months ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

As Mike says, this isn't an edgeR question. But I will pretend it is. If you have the counts, go through an edgeR analysis - or at least to calling glmFit - with the following design matrix:

group <- c("M", "M", "N", "N")
design <- model.matrix(~0 + group)


You didn't specify the nature of your replicates, but you may need to add a blocking factor if M1 is related to N1 (e.g., from the same individual) and M2 is related to N2.

Anyway, once you've done that, you can obtain the log-average expression of each level of group from the \$coefficients field of the output of glmFit. This provides a general approach to getting condition-specific expression values, taking advantage of NB GLMs to give a more precise estimate than averaging FPKMs.

Thank you very much!!

Answer: Representvie gene expression value in one condition with several replicates
4
16 months ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

If you want expression values on a log-scale, then you can use the process explained by Aaron, which is similar to but better than just averaging the individual log-expression values.

If you want expression values on the unlogged scale, then the edgeR package provides functions to do this. Type

library(edgeR)
?cpmByGroup
?rpkmByGroup


Thank you very much for you advice!

Answer: Representvie gene expression value in one condition with several replicates
0
16 months ago by
Michael Love22k
United States
Michael Love22k wrote:

This isn't a DESeq2 (or edgeR) question really, so I'm removing the DESeq2 tag. The arithmetic or geometric mean of the TPM seems to be a reasonable number for the average relative abundance. I don't have any strong opinions about this though.