I am working with RNA seq data from TCGA using TCGAbiolinks. Everything has been working fine so far and suddenly I get this error:
> RnaseqSE <- GDCprepare(query) |=================================================================================| 100% Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column
I don't think I changed anything in the code. Also, as suggested here, I changed the query to:
RnaseqSE <- GDCprepare(query, save=TRUE, save.filename = "Gene_Expression_Quantification.rda", summarizedExperiment = FALSE)
and I get it running, however, my next command fails,
Matrix.C1 <- assay(RnaseqSE,"raw_count") Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"data.frame", "character"’
Any help would be appreciated. Thanks!