Question: Can I used GFOLD or EdgeR to identify DEG in a time-course type experiment with no replication?
gravatar for alexandra.lanot
3.1 years ago by
alexandra.lanot0 wrote:

Dear all, I am new to Bioinformatic but I hope my question will make some sense. I need to analyse my RNASeq data: 7 samples corresponding to different developmental stages but no replication (I know that this is bad). I was thinking of using EdgeR or GFOLD. Most of the information I have seen is to compare two samples. I need to compare them as a whole as I would be interested in genes expressed in only a few of the samples.
Can I use GFOLD for comparison of more than 2 samples? Can I used EdgeR for comparison of more than 2 samples knowing I have no replication? Many thanks in advance A

rna-seq • 740 views
ADD COMMENTlink modified 3.1 years ago by WouterDeCoster38k • written 3.1 years ago by alexandra.lanot0
gravatar for WouterDeCoster
3.1 years ago by
WouterDeCoster38k wrote:

Replicates are really required for differential expression analysis. Perhaps you can convince one of the tools to work for your poor experimental setup, but I would trust any data coming from that. Would it make sense in your design to compare the 3 first with the 4 last timepoints?

ADD COMMENTlink written 3.1 years ago by WouterDeCoster38k
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