Getting the actually expression values in a DEG analysis
Hello,
When doing a differentially expressed genes analysis in limma and using the toptables() function to get the results you do not get the actually expression level changes, just the fold change. Is there anyway to get the actually expression level change? Thanks.
• 3,075 views
•
link
0 answers
No answers yet.
Log in to answer this question.
What do you mean by "expression level change"?
are you referring to the normalized expression values for your samples? then upon normalization you can put the normalized values to a vector which can be saved as a matrix and should be giving you the desired output you are asking for. This is what I can make from your question
In any case if you create the expression matrix which are basically normalized value of the genes across samples, either RPKM(single-end) , FPKM (paired-end) or TPM , then you will have so called expression values for all genes across all samples. Once you have the list of DEGs you can use this list to fetch the expression values of all the DEGs acorss all your samples that groups the DE analysis samples. This is a very straight-forward approach used for heatmap generation as well.
Sorry I should mention I am using microarrays. I assume to what you are saying you should use some sort of shell script to match your DEG to you normalized list? Do you know of a way to do it automatically through limma?