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rli012 / GDCRNATools

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC
Apache License 2.0
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Error in rna.expr[pc, ] : subscript out of bounds #13

Open maxlarosa opened 4 years ago

maxlarosa commented 4 years ago

When I try the following code

library(GDCRNATools) library(limma) data(lncTarget) data("pcTarget") data("DEGAll") data("mirCounts") data("rnaCounts")

Normalization of RNAseq data

rnaExpr <- gdcVoomNormalization(counts = rnaCounts, filter = FALSE) ####### Normalization of miRNAs data ####### mirExpr <- gdcVoomNormalization(counts = mirCounts, filter = FALSE)

deLNC <- gdcDEReport(deg = DEGAll, gene.type = 'long_non_coding') dePC <- gdcDEReport(deg = DEGAll, gene.type = 'protein_coding') ceOutput <- gdcCEAnalysis(lnc = rownames(deLNC), pc = rownames(dePC), lnc.targets = lncTarget, pc.targets = pcTarget, rna.expr = rnaExpr, mir.expr = mirExpr)

I get this error: Error in rna.expr[pc, ] : subscript out of bounds

MaiTian-li commented 3 years ago

Hello! Have you solved this problem now ？I encountered the same error with Error in mir.expr[mir, ] : subscript out of bounds. If you already know why and how to avoid such an error, I appreciate your reply!