TCGAAnalyze_DEA Issue, "Error in names"
0
0
Entering edit mode
Gandino • 0
@844ff225
Last seen 2.9 years ago
Italy

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",
  • paired=FALSE)

And it gives: "Errore in names(x) <- value : l'attributo 'names' [7] dev'essere della stessa lunghezza del vettore [1]" .

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?

miRNAseq TCGAbiolinks TCGAAnalyze_DEA • 828 views
ADD COMMENT

Login before adding your answer.

Traffic: 521 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6