Question: Best statistical test for 1 vs 2 replicates
0
gravatar for from the mountains
2.7 years ago by
United States
from the mountains80 wrote:

Hello all,

I have to do a comparison of two groups. The first group has 1 sample and the second group has 2 samples. What is the most appropriate statistical test/software for this comparison? The resources that are most readily available to me are:

  1. DeSeq2
  2. Baggerly's test (test on proportions
  3. Edge (Edge R basically)
  4. I have a Gaussian model but I have never tried it out before.

I know 1 vs 2 is not ideal, but it's the challenge I've been given. I reason that DeSeq2 needs ideally 3 replicates per group and 2 replicates per group is pushing it. Not sure which of the rest is most appropriate.

Help would be very much appreciated. Thanks!

rna-seq • 867 views
ADD COMMENTlink modified 2.7 years ago by h.mon29k • written 2.7 years ago by from the mountains80

There is no good solution for such a low number of/no replicates. Which method is appropriate depends on the source of your data. I am guessing RNA-seq according to the tag. You can try both edgeR and Deseq but you risk having no significant genes.

ADD REPLYlink written 2.7 years ago by Michael Dondrup47k

thanks! yes, it is RNA-seq.

ADD REPLYlink written 2.7 years ago by from the mountains80
0
gravatar for h.mon
2.7 years ago by
h.mon29k
Brazil
h.mon29k wrote:

You may try GFOLD or NoiSeq, both were designed for few or no replicates.

ADD COMMENTlink written 2.7 years ago by h.mon29k

thank you! i will have to put that in my repertoire.

ADD REPLYlink written 2.7 years ago by from the mountains80
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