Exprimental design for DESeq2 or edger
Hi
I have 3 different patients : one cancer and two controls
But for cancer I have two time points
I want to know differentially expressed genes beween these time points
I even don't know how to phrase this to search in google
Samples condition
CS001_time point 1 cancer
CS001_time point 2 cancer
HC002 control
HC003 control
Please give me an idea how I get differentially expressed genes between these time points
Thank you in advance
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Cross-posted to https://support.bioconductor.org/p/9134936/
With only one replicate for each time point, there's not a lot you can do that's mathematically justifiable.
Sorry what if we have two technical replicates for each of these I mean actually I have 2 rounds of sequencing to give greater read depth for each of these
like
Technical replicates are usually collapsed, and not treated as biological replicates in the case of differential expression.
You can't sequence the same thing over and over again and pretend you have a handle on biological variation.
Sorry does it make any sense to first compare CS001_t1 and CS002 versus HC002 and HC003
then CS001_t2 and CS002 versus HC002 and HC003
and then take uncommon differentially expressed genes as related to time points?
I mean comparing time point 1 plus to another cancer sample versus two controls in one go
and comparing time point 2 plus to another cancer sample versus two controls in next go
And finally comparing the results
You can't play math games to get around a lack of replicates.