Entering edit mode
3.6 years ago
whytrykillme
•
0
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
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
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?
Fine too.
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