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Calculating fold change

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

genome
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updated by Biostar Biostar • written by amir.007.taherkhani • amir.007.taherkhani

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).

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written by Devon Ryan Devon Ryan

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?

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written by WouterDeCoster WouterDeCoster

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?

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written by naloy • naloy

Please post questions as questions rather than as comments.

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written by Devon Ryan Devon Ryan

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