I have a data in the form of a dataframe that I downloaded from GTEx Portal. It contains RNASeq gene read counts used in their study.
> dim(expr.df)  55993 2921 > expr.df[1:10,1:2] GTEX-N7MS-0007-SM-2D7W1 GTEX-N7MS-0008-SM-4E3JI ENSG00000223972 0 0 ENSG00000227232 158 166 ENSG00000243485 0 0 ENSG00000237613 0 0 ENSG00000268020 0 0 ENSG00000240361 0 0 ENSG00000186092 0 0 ENSG00000238009 17 2 ENSG00000233750 35 0 ENSG00000237683 8489 34
I checked the sample information file and there is no information about the conditions. I want to normalize the raw counts. For that, I want to use DESeq's
getVarianceStabilizedData() function. However this function takes as an input a
CountDataSet object. So when I try to make a
CountDataSet object using this:
> cds <- newCountDataSet(countData = as.matrix(expr.df)) Error in is(conditions, "matrix") : argument "conditions" is missing, with no default
It spits out an error asking me to specify the conditions. However, there are no conditions in this dataset. How can I normalize these values?