Hi All,
I've been analysing RNA-Seq data for differentially expressed genes with DESeq & Partek, and I have a few questions:-
i) Is it a good idea to filter out genes which are expressed at a very low level? - Sometimes a gene is flagged as being differentially expressed and then when I go back to the raw data I find that the read count is only, say, 5.
ii) Partek appears to use ANOVA. Having read some of the discussion about using the poisson or negative binomial distribution for count data, is ANOVA a valid statistical test for this kind of data?
Many thanks in advance.
Adam
I've been analysing RNA-Seq data for differentially expressed genes with DESeq & Partek, and I have a few questions:-
i) Is it a good idea to filter out genes which are expressed at a very low level? - Sometimes a gene is flagged as being differentially expressed and then when I go back to the raw data I find that the read count is only, say, 5.
ii) Partek appears to use ANOVA. Having read some of the discussion about using the poisson or negative binomial distribution for count data, is ANOVA a valid statistical test for this kind of data?
Many thanks in advance.
Adam
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