Entering edit mode

3.0 years ago

Susmita Mandal
▴
100

Hello everyone,

I am doing expression analysis on samples having different cell types and their conversions. While doing the fold change of few genes w.r.t. to one cell type, I am getting some negative values of few genes in the other cell types and thus I cannot include them in the log2 FC plot. I would like to incorporate those genes into the plot? Is there any way or I have to remove them and make the plot (sadly)?

Thanks in advance, Susmita

Explanation: Imagine two values, x and y, and you divide them by each other

`(x/y)`

there are two options if values are not logged:Obviously compressing values between 0 and 1 is not optimal. This is evident when you plot values from option 1 and 2, which will result in a highly assymetrical graph (because the space from 1 to Inf is visually larger than between 0 and 1). Therefore, one uses

`log2(x/y)`

which will transform fold changes from option 2 into a range of equal size as option 1.You should note that no negative values can be calculated from non-logged count data., as any x < y will be somewhere between 0 and 1.