Hello,
I am new to using R and have wanted to use to analyze expression data from TCGA. Right now I am using TCGAbiolinks and I am following their documentation on miRNA expression analysis.
I have made a few changes to code outlined there to fit analyzing the L-AML dataset, which is as follows:
Getting L-AML data
require(TCGAbiolinks) LAMLdata <- "TCGA-LAML" DataDirectory <- paste0("LAML", gsub("-", "_", LAMLdata)) FileNameData <- paste0(DataDirectory, "_", "miRNA_gene_quantification" , ".rda")
query.miR <- GDCquery(project = LAMLdata, data.category = "Transcriptome Profiling", data.type = "miRNA Expression Quantification")
samplesDown.miR <- getResults(query.miR, cols=c("cases"))
dataSmTRBM.miR <- TCGAquery_SampleTypes(barcode = samplesDown.miR, typesample = "TRBM")
dataSmNBM.miR <- TCGAquery_SampleTypes(barcode = samplesDown.miR, typesample = "NBM")
dataSmTRBM_short.mir <- dataSmTRBM.miR[1:10]
dataSmNBM_short.mir <- dataSmNBM.miR[1:10]
queryDown.miR <- GDCquery(project = LAMLdata, data.category = "Transcriptome Profiling", data.type = "miRNA Expression Quantification", barcode = c(dataSmTRBM_short.mir, dataSmNBM.miR))
GDCdownload(query = queryDown.miR, directory = DataDirectory)
dataAssay.miR <- GDCprepare(query = queryDown.miR, save = TRUE, save.filename = FileNameData, summarizedExperiment = TRUE, directory = DataDirectory)
rownames(dataAssay.miR) <- dataAssay.miR$miRNA_ID
using read_count's data
read_countData <- colnames(dataAssay.miR)[grep("count", colnames(dataAssay.miR))] dataAssay.miR <- dataAssay.miR[,read_countData] colnames(dataAssay.miR) <- gsub("read_count_", "", colnames(dataAssay.miR))
dataFilt <- TCGAanalyze_Filtering(tabDF = dataAssay.miR, method = "quantile", qnt.cut = 0.25)
dataDEGs <- TCGAanalyze_DEA(mat1 = dataFilt[,dataSmNBM_short.mir], mat2 = dataFilt[,dataSmTRBM_short.mir], Cond1type = "Normal", Cond2type = "Tumor", fdr.cut = 0.01, logFC.cut = 1, method = "glmLRT")
When I source the code, I am ultimately met with this error:
Error in [.data.frame(dataFilt, , dataSmNBM_short.mir) :
undefined columns selected
What I have noticed is that dataSmNBM.miR and dataSmTRBM.miR have a character (empty) value assigned to them, and thus I suspect this to be the first cause of my woes.
Can someone explain to me where things might have gone awry? I have gone over the code multiple times and have consulted documentation and everything still seems to be logical to me.
Thank you for your time and many thanks!
