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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Need help with one error #488

Open shahabusmani opened 2 years ago

shahabusmani commented 2 years ago

Hi, I have started learning TCGA biolink and started with miRNA vignette. Currently facing a problem with the following line. Also pasting the error I am getting (The completed code is same as given in vignette:https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/analysis.html)

dataAssy.miR <- dataAssy.miR[,read_countData]

Error in [.data.table(dataAssy.miR, , read_countData) : j (the 2nd argument inside [...]) is a single symbol but column name 'read_countData' is not found. Perhaps you intended DT[, ..read_countData]. This difference to data.frame is deliberate and explained in FAQ 1.1.

shahabusmani commented 2 years ago

This has been solved. Currently the inputs are taken as follows: dataAssy.miR <- dataAssy.miR[,..read_countData]

*I need to add two dots (..) to read the second argument.
But now following command is giving null table which I couldn't understand: dataFilt <- TCGAanalyze_Filtering(tabDF = dataAssy.miR, method = "quantile", qnt.cut = 0.25)

Below is the screenshot of dataAssy.miR image