How to run vst transformation
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sropri • 0
@af8dfadb
Last seen 4 days ago
United States

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.

RNASeqData vst • 126 views
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@mikelove
Last seen 1 day ago
United States

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

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