TCGA2STAT Error: Firehose connection

Question

[Gnana]

rnaseq.ov <- getTCGA(disease="OV", data.type="RNASeq", type="RPKM")
Error: Problem connect to Firehose. Please ensure Internet connection is working.

[Ram]

Read the error message

[Gnana]

I'm very new to this R programming so, i was wondering if i have to do something else in this case like manually connect firehose. Because my internet is working fine.

[Ram]

What's the output to sessionInfo() on your R session?

[Gnana]

sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_India.utf8  LC_CTYPE=English_India.utf8    LC_MONETARY=English_India.utf8
[4] LC_NUMERIC=C                   LC_TIME=English_India.utf8

time zone: Asia/Calcutta
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] TCGA2STAT_1.3.1

loaded via a namespace (and not attached):
[1] compiler_4.3.1    tools_4.3.1       rstudioapi_0.15.0 XML_3.99-0.14

[Ngrin]

Hey Gnana, could you find a way to solve the issue? I have the same error

[Ram]

The package has been removed from CRAN and BioConductor. Should you even be using it?

[Ngrin]

Yeah makes sense. I was following their github. Thanks for pointing this out.

[Ram]

If their github repo is alive, raise an issue there.

[LauferVA]

agree.

from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from one of several sources. as an example that also has attendant R packages, consider cBioportal.

if you tell us exactly what you are trying to download, we can help with a workaround.