Closed lwaldron closed 3 years ago
Yes, I also observe sample numbers to be too low and not in agreement with the actual sample number provided by Broad Firehose itself, as eg for SARC
http://firebrowse.org/?cohort=SARC&download_dialog=true
> x <- curatedTCGAData(diseaseCode = "SARC", assays = "RNASeqGene", FALSE)
Error in curatedTCGAData(diseaseCode = "SARC", assays = "RNASeqGene", :
Cancer and data type combination(s) not available
> x <- curatedTCGAData(diseaseCode = "SARC", assays = "RNASeqGeneNorm", FALSE)
Error in .searchFromInputs(assays, assaysAvail) :
No matches found, modify search criteria
This looks like it was returning Level_3__gene_expression__data
when we intended to provide Level_3__RSEM_genes__data
. This accounts for the discrepancy.
We now have RNASeqGene
and RNASeq2Gene
options in RTCGAToolbox and in version = "2.0.0"
for curatedTCGAData
.
See data release version 2.0.0
in devel version 1.13.1
(commit 5da7bea5d6e2b316f50f8ba957d0dc98e0c596c8)
> getFirehoseData("COAD", RNASeqGene=TRUE, clinical = FALSE)
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COAD/20160128/gdac.broadinstitute.org_COAD.Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 3593305 bytes (3.4 MB)
==================================================
downloaded 3.4 MB
gdac.broadinstitute.org_COAD.Merge_rnaseq__illuminaga_rnaseq__unc_edu__Level_3__gene_expression__data.Level_3.2016012800.0.0
RNAseq data will be imported! This may take a while!
Start: 2020-11-30 14:31:58
Done: 2020-11-30 14:31:58
COAD FirehoseData objectStandard run date: 20160128
Analysis running date: NA
Available data types:
RNASeqGene: A matrix of count or normalized data, dim: 20502 x 10
To export data, use the 'getData' function.
##
> getFirehoseData("COAD", RNASeq2Gene=TRUE, clinical = FALSE)
trying URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COAD/20160128/gdac.broadinstitute.org_COAD.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 49751986 bytes (47.4 MB)
==================================================
downloaded 47.4 MB
gdac.broadinstitute.org_COAD.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes__data.Level_3.2016012800.0.0
RNAseq2 data will be imported! This may take a while!
Start: 2020-11-30 14:32:45
Done: 2020-11-30 14:32:47
Using locally cached version of /tmp/RtmpiJLElh/20160128-COAD-RNAseq2Gene.txt
RNAseq2 data will be imported! This may take a while!
Start: 2020-11-30 14:32:53
Done: 2020-11-30 14:32:55
COAD FirehoseData objectStandard run date: 20160128
Analysis running date: NA
Available data types:
RNASeq2Gene: A matrix of count or scaled estimate data, dim: 20501 x 191
To export data, use the 'getData' function.
See #38 for details
Do a human check to make sure this is correct - only 10 samples for RNASeqGene? It seems to be in low numbers or not present for other datasets as well.