How to properly average normalized counts of biological replicates
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Marina • 0
@marina-15019
Last seen 6 months ago

Dear all, I'm trying to combine the normalized counts from 3 biological replicates into single columns of the normalized count matrix. I need it in order to "absolutely" analyze the expression of specific genes, for example - presenting expressions on heat maps (or other plots) and doing co expression analysis. I would like to emphasize that all 3 biological replicates are, in my point of view, identical, meaning, all are before any treatment, or all of them are after a specific treatment. Yet, I cannot treat them as technical replicates as they were taken from different biological samples. I know that Deseq2 can collapse technical replicates into a single column, but it is not intended for biological replicates (and I must say that I'm not fully understand why, if all "averaged" replicates represent the same treatment but I'm still a newbie and I accept the verdict). What alternatives do I have? Is it allowed to do a simple average on the normalized counts of each of the 3 samples converting it into a single normalized count?? Any suggestion would be highly appreciated.

DESeq2 Normalization RNASeqR • 385 views
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@mikelove
Last seen 1 day ago
United States

If you want to calculate the average normalized count for a group of samples:

ave.cnt.A <- rowMeans( counts(dds, normalized=TRUE)[ , dds\$condition == "A" ] )

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Thank you so much!! I'll try that. If I understand correctly then a simple average of the 3 (for example) normalized count columns is what I need to do? For some reason, I had in my mind that a more careful averaging was required, something that takes into consideration some additional statistical properties, but I have no idea why I was thinking this way...

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"is what i need to do"?

Yes to calculate the average scaled count, the above is the code you would use.