Hi guys,

I filtered out my raw count data for my gene list by filtering genes with <5 counts in at least 90% of all samples. Now I have a data frame with genes as rows and counts in 81 samples as columns. I tried running variance stabilizing transformation (vst) on this data frame by using the following code :

varianceStabilizingTransformation(myFilt, blind = FALSE)

However, I am getting this error:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘estimateSizeFactors’ for signature ‘"data.frame"’

I know there are other posts that asked similar questions and I have tried to understand them but am still confused on why it is not working and giving me this error. Please, any help is appreciated.

Convert to matrix or dds. See the man page on the inputs.