Entering edit mode
7.0 years ago
amir.007.taherkhani
▴
10
Hi everyone i am confused with a very simple problem..!! How to determine fold change when the median (or an average) of one or two groups having negative values? Suppose 2 expression values A,B (treatment): A= -3 b= +2
or
A= -3 B= -2
What do the numbers represent? My guess is that these are log transformed, in which case the log fold-change is the difference in values (e.g., A=-3, B=2 would then be 5).
And how did you obtain negative expression values? RNA-seq would be count data, which is never negative. Microarrays are light intensity, which also shouldn't be negative. Or did I misunderstand? Are those numbers already normalized/transformed?
Fold change is a ratio of number of aligned or classified transcripts in the treatment condition and the control condition. As the number of transcripts can never be negative, I wonder why are some of our fold change values are negative (not after log2 transformation!)
Could somebody please explain this?
Please post questions as questions rather than as comments.