If the workflow has changed to STAR-counts, when we use the parameter geneInfo of the function(TCGAanalyze_Normalization) can we use the geneInfoHT？I means in R Documentation that the geneInfoHT is for normalization of HTseq data.
Next step:
COAD_dataFilt <- TCGAanalyze_Filtering(tabDF = COAD_dataNorm, method = "quantile", qnt.cut = 0.25)
Error in quantile.default(rowMeans(tabDF), qnt.cut) :
missing values and NaN's not allowed if 'na.rm' is FALSE
Hello！Tiago. AS you know TCGA has change the workflow from the HTseq data to STAR-counts. So I am confused when I use the function following:
COAD_dataNorm <- TCGAanalyze_Normalization( tabDF = COAD_dataPrep, geneInfo = geneInfoHT, method = "gcContent" )If the workflow has changed to STAR-counts, when we use the parameter
geneInfoof the function(TCGAanalyze_Normalization) can we use the geneInfoHT？I means in R Documentation that the geneInfoHT is for normalization of HTseq data.Next step:
COAD_dataFilt <- TCGAanalyze_Filtering(tabDF = COAD_dataNorm, method = "quantile", qnt.cut = 0.25)Error in quantile.default(rowMeans(tabDF), qnt.cut) : missing values and NaN's not allowed if 'na.rm' is FALSE