DESeq2, coldata parameter

Question

[Morris_Chair]

Hello,

I want to use DESeq2 to compare the expression profiling of 2 cells line of the same type of tumor. Basically I have 2 bam files and I want to see which are the top genes differentially expressed between them. I don't have a control and I don't have a treatmnent.

My question is, how should I set up the coldata command?

coldata = data.frame(row.names = c(....

and the condition?

e.g

(condition <- factor(c(rep("ctl", 4), rep("exp", 4))))

Thank you

[Morris_Chair]

Ok, so what it the minimum (biological replicates ) samples that I have to compare?

thanks

[ATpoint]

Technically it would be n=2 so that at least the dispersion can be somewhat estimated. n=3 is of course better and generally accepted as the minimum for meaningful statistics but depending on the biological variability in your data, you might need more to get significant results.

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

Generally, the minimum number of replicates is considered to be 3. But if you can afford more your analysis will be better. In addition, if you only have three you cannot really handle the case when one sample fails in the library prep/sequencing.

Answer 1

[WouterDeCoster]

As you have been told before you cannot do a meaningful differential expression analysis with a 1-vs-1 comparison.