In a recent project, I used the BioC package RTCGAToolbox to conveniently fetch data from TCGA.
I now would like to download miRNA expression data for the TCGA AML patient cohort. However, while I can successfully download all other data types, miRNA expression profiles are not retrieved.
A call to (tested with any runDate)
getFirehoseData(dataset = 'LAML', runDate = '20160128', forceDownload = TRUE, miRNASeq_Gene = TRUE, miRNA_Array = TRUE)
fetches only the clinical data. In contrast, setting other arguments to TRUE (e.g.
RNAseq2_Gene_Norm = TRUE or Mutation = TRUE) works very well. Neither
fileSizeLimit nor the project date are an issue here - I tried several.
One thing I noticed in the getFirehoseData function is that the internal function
.getLinks is called with different arguments if
RNAseq2_Gene_Norm=TRUE or if
miRNASeq_Gene=TRUE. Not sure how relevant this is, though.
I contacted the developer but I didn't get an reply, yet. Thank you very much for your help.
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.12.3 (Sierra) locale:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  RTCGAToolbox_2.2.2 loaded via a namespace (and not attached):  RCircos_1.1.3 Matrix_1.2-7.1 limma_3.28.21 formatR_1.4 tools_3.3.1  RCurl_1.95-4.8 survival_2.40-1 RJSONIO_1.3-0 splines_3.3.1 grid_3.3.1  data.table_1.9.6 knitr_1.14 chron_2.3-47 bitops_1.0-6 lattice_0.20-34  XML_3.98-1.4