Entering edit mode
Hi,
i downloaded TCGA-OV data from TCGAbiolinks:
query <- GDCquery(project = c("TCGA-OV"),
data.category = "Transcriptome Profiling",
legacy = FALSE,
data.type = "Gene Expression Quantification",
sample.type = "Solid Tissue Normal",
workflow.type = "HTSeq - Counts")
GDCdownload(query)
gene_exp <- GDCprepare(query, summarizedExperiment = FALSE)
the result is:
Sorry! There is no result for your query. Please check in GDC the data available or if there is no error in your query.
But on GDC i see 71 solid tissue normal cases. Moreover, in other cases the number of samples do not match between TCGAbiolinks download and GDC cases.
Any suggenstions?
Thanks!
You can see normal samples for HTSeq counts here:
71 normal tissue cases
No, those are all tumour. On the original link that you posted, the normal samples in the list were from DNA sequencing, not RNA-sequencing.
Can see here, too, on Xena:
The barcodes for HTSeq counts for TCGA-OV indicate that they are all primary tumour.
Ok, therefore RNA-seq checkbox not works as a filter on GDC? if I select solid tissue normal the result refers to all normal tissue independently from data category or data type selected?
Thank you Kevin!