Question: limitations of Edge R or DEseq
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gravatar for maryak
9 months ago by
maryak10
maryak10 wrote:

Are there any limitations of Edge R or DEseq while doing differential gene expression analysis?

rna-seq gene • 677 views
ADD COMMENTlink modified 9 months ago by waqaskhokhar99960 • written 9 months ago by maryak10

Can you elaborate on why you're asking this? Which problem do you have? It's a quite broad question and it's unclear what you are looking for.

ADD REPLYlink written 9 months ago by WouterDeCoster40k
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0
gravatar for waqaskhokhar999
9 months ago by
waqaskhokhar99960 wrote:

DESeq is not suitable if you don't have biological replicates but EdgeR can calculate differential gene expression even you don't have biological replicates.

ADD COMMENTlink written 9 months ago by waqaskhokhar99960
3

Differential expression without replicates is never valid, regardless of the method you use.

ADD REPLYlink written 9 months ago by WouterDeCoster40k

In case you want to see DE among large number of samples and you don't have replicates you can use EdgeR. Please see the section 2.11 What to do if you have no replicates

ADD REPLYlink written 9 months ago by waqaskhokhar99960
3

That is true waqas; however, it is bad practice. Results from single replicate experiments would suffer a lack of reproducibility. Not your fault, of course, but the EdgeR authors should probably reflect on the leadership position that they hold and be aware that the things they say/write can be interpreted in different ways.

ADD REPLYlink written 9 months ago by Kevin Blighe47k
2

Not only is it bad practice it is misleading - the whole reason we do DE is to have an idea of whether a result will extrapolate to other samples analyzed. Without independent biological replicates no such claims can be made. The 2.11 section of the edgeR vignette should only be used for pilot studies and never published!

ADD REPLYlink written 9 months ago by kristoffer.vittingseerup2.2k
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From the link:

  1. Be satisfied with a descriptive analysis, that might include an MDS plot and an analysis of fold changes. Do not attempt a significance analysis. This may be the best advice.
ADD REPLYlink written 9 months ago by ATpoint21k
1

" to see DE among large number of samples". Sounds like you have replicates to me. See my answer here: A: Replicates for RNA-seq from 1 cell line undergoing different treatments

ADD REPLYlink written 9 months ago by i.sudbery5.2k
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