This is a test version of Biostars. For the public version, visit https://www.biostars.org.
calculating fold change from dataframe

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!

fold frame change data
• 1,243 views • link
updated by ATpoint ATpoint • written by Gil Rodriguez • Gil Rodriguez

1 answer

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.

• 0 views • link
written by ATpoint ATpoint

Log in to answer this question.

More posts like this