Hi I have a question about the use of the contrast of DESeq2.
If I have 3 (or more) conditions: A, B and C and I want to do: A vs C and B vs C
I can create a table with the columns A B C and to use the contrast on it. With this approach i can compare the FC of the two comparisons
If I made the tables A B and B C and I wanted to do: A vs C and B vs C now is it wrong to compare the FC of the two a comparisons?
Thank you.
Generally we recommend putting all the samples from all the different conditions into one dds object, then running DESeq(), then making comparisons with results(). The estimation of dispersion can often be better when you create one big dds object.
Thank you. I have another question. If my raw data table contains very low value, for example 1 reads only in one sample, is it better to filter the table before the normalization or such values are important for the statistical model?