Entering edit mode
6.4 years ago
Björn
▴
110
Hi, For mRNA DE expression, the code used is
dataNorm <- TCGAanalyze_Normalization(tabDF = dataPrep,
geneInfo = geneInfo,
method = "gcContent")
However, what should I use for miRNAs in
dataNorm <- TCGAanalyze_Normalization(tabDF = dataPrep,
geneInfo = ??,
method = "??")
Next question Is there a way to use "TMM" instead of "quantile" during filtration ?
dataFilt <- TCGAanalyze_Filtering(tabDF = dataNorm,
qnt.cut = 0.25,
method='quantile')