I have a total of twelve samples
3 replicates per condition
Mutant(3) and Wild-Type(3) in exponential
Mutant(3) and Wild-Type(3) in stationary
Before I submit the raw counts to DESeq2 for Mutant/WT(exponential) comparison, in one of the genes the counts are more for the Mutants in the exponential condition than in Wild-Type
After running DESeq2 and getting the results and normalized counts, the counts are flipped and the change is insignificant.
In comparing ALL FOUR in contrasting I find the normalized counts are flipped from the original raw counts but the results this time are significant.
Which one do I go with? Why would the raw counts be completely flipped?
It's literally the difference between positive and negative regulation...
I took the normalized raw counts from the comparison between all four conditions and did my own glm.nb analysis and found that this is a statistically significant change... I would not have found this if it was from the normalized counts from the comparison between two conditions... Moreover, the counts are completely flipped... Any thoughts on this?
I guess flipping of counts happens a lot as I look at it more closely which has a lot to do with the size factor but which comparison is correct? Do I go with significant or insignificant... I am sort of lost on this....
3 replicates per condition
Mutant(3) and Wild-Type(3) in exponential
Mutant(3) and Wild-Type(3) in stationary
Before I submit the raw counts to DESeq2 for Mutant/WT(exponential) comparison, in one of the genes the counts are more for the Mutants in the exponential condition than in Wild-Type
After running DESeq2 and getting the results and normalized counts, the counts are flipped and the change is insignificant.
In comparing ALL FOUR in contrasting I find the normalized counts are flipped from the original raw counts but the results this time are significant.
Which one do I go with? Why would the raw counts be completely flipped?
It's literally the difference between positive and negative regulation...
I took the normalized raw counts from the comparison between all four conditions and did my own glm.nb analysis and found that this is a statistically significant change... I would not have found this if it was from the normalized counts from the comparison between two conditions... Moreover, the counts are completely flipped... Any thoughts on this?
I guess flipping of counts happens a lot as I look at it more closely which has a lot to do with the size factor but which comparison is correct? Do I go with significant or insignificant... I am sort of lost on this....
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