Entering edit mode
6 months ago
michelafrancesconi9
▴
20
Hello everyone!
I have bulk rna-seq data and would like to do some analysis to see what cell types I have, with the MCP-counter package. However, they require that the matrix be normalized with frma in r and here I am running into problems.
I have a data matrix and in order to normalize it in frma it has to be "AffyBatch," "ExonFeatureSet," "GeneFeatureSet" objects. I've been trying for days but I don't understand how to do it.
I installed affy but when I try to use the function:
affy_obj <- AffyBatch(data = as.matrix(matrixFiltered))
Error in AffyBatch(data = as.matrix(matrixFiltered)) :
can't find the function "AffyBatch"
Do you know why? What I have to do?
Thank you
Did you load the package using
library(affy)
after installing it?yes, but nothing change
Please show your full code as well as the output to
sessionInfo()
Include your full code (with the steps where you load the package, call the function and face the error).
I read the docs, and
AffyBatch
is a class, not a function. Useread.affybatch()
orReadAffy()
to create theAffyBatch
object from input files.https://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/affy/html/AffyBatch-class.html
Yes! But now I have this error
Sorry, I changed my comment after I wrote that
affy::AffyBatch
part. Please try the new solution I posted. It will probably not work with yourmatrixFiltered
object - you'd probably need to read in the files directly.I have two different errors now:
Please read my reply to your other comment. This is as far as I can help you.
I download my matrix and I try to read it and upload it on R through the function that suggest but nothing change
This is not required,
sessionInfo()
covers what's required while leaving out what's not.