Question: DESeq2 with one sample eliminated
0
gravatar for whytrykillme
6 weeks ago by
whytrykillme0 wrote:

I have 11 samples currently. Initially there were supposed to be three replicates of each group or factor. To remedy this I tried to use the instructions here for levels without samples but I don't think it works for me http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#levels-without-samples

How do you navigate this issue?

     Factor.    Condition
1.  A            1
2.  A            1
3.  B            1
4.  B            1
5.  B            1
6.  C            2
7.  C            3
8.  C            2
9.  D            3
10. D            2
11. D            3
rna-seq deseq2 • 156 views
ADD COMMENTlink modified 6 weeks ago by umekage0 • written 6 weeks ago by whytrykillme0
1

You can proceed as normal. It is more important that you have 3 of any sample, rather than 3 per group. For example, you could have 2 for condition A and 1 for condition B, and this would be okay.

Kevin

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Kevin Blighe66k
1

It is more important that you have 3 of any sample, rather than 3 per group.

That sounds so ... odd. Is the number only useful for statistics on the housekeeping genes? What if you had 3 conditions and one sample per condition?

ADD REPLYlink written 6 weeks ago by RamRS30k
1

Fine too.

ADD REPLYlink written 6 weeks ago by Kevin Blighe66k
1

I think that I am showing signs of 'wear and tear' because I answered this and completely missed the point of the question. Moved back to a comment

ADD REPLYlink written 6 weeks ago by Kevin Blighe66k
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