I'm trying to use TCGABiolinks package to analyze a table containing raw count of miRNA-seq isoform data converted in mature. The pipeline works fine until the "TCGAanalyze_DEA" function wich gives this error:
>dataDEGs <- TCGAanalyze_DEA(mat1 = dataFilt[,dataSmNT_short.miR],
- mat2 = dataFilt[,dataSmTP_short.miR],
- Cond1type = "Normal",
- Cond2type = "Tumor",
- fdr.cut = 0.1,
- logFC.cut = 1.3,
- method = "glmLRT",
And it gives: "Errore in names(x) <- value : l'attributo 'names'  dev'essere della stessa lunghezza del vettore " .
I suppose that the two vectors "dataSmNT_short.miR" and "dataSmTP_short.miR" with two different list of samples couldn't extract the two matrix "mat1" and "mat2" beacause they didn't have the same number of samples of the "dataFilt" dataframe columns, but when I run "mat1 = dataFilt[,dataSmNT_short.miR]" and "mat2 = dataFilt[,dataSmTP_short.miR]" I obtain the two matrix correctly.
So I don't know whats the problem, I can only think that this happens beacause I didn't run the steps wich download the raw data directly with the TCGABiolinks package, is that possible? Can't I use a table of raw data loaded externally to use the "TCGAanalyze_DEA" function?