calculating fold change from dataframe

Question

[Gil Rodriguez]

Hey,

is there a code or a way to calculate the fold change? all i could found is a calculations that includes only two variables, for example:

log2FC=Log2(B)-Log2(A)

but i have a data frame and i want to found the value , my data frame has more than two varables (i have more than one column for "healthy" and more than one column for "cancer")

it looks for example like this:

Gene	Healthy 1	Health 2	healty 3	cancer 1	cancer 2
A	3	4	4	5	6
B	4	5	4	2	1
C	0	8	7	2	3

i want to do it in order to make a volcano plot graph (if there is a way to avoid it, and add an graph based on other parametes i would be happy to hear from you as well)

thanks!

Answer 1

[ATpoint]

What kind of data is this? The most straight-forward and also most statistically-sound way would be to plug it into a differential analysis framework such as DESeq2 or limma and then use the moderated fold changes these tools produce.