Open jpmam1 opened 6 years ago
It appears GTEx replaced the static locations for their data. I'm going to have to figure a work-around for that. In the meantime, you can manually go to https://www.gtexportal.org/static/datasets/ (login) and download the files and load them in following the script within downloadGTEx.
I am still getting the same error as @jpmam1 when trying to download other GTEx data, apart from the example (skin dataset). @jnpaulson is there an update with the work-around for this?
Are you getting it through dbGaP, or elsewhere?
On Tue, Jan 9, 2018 at 6:48 PM, Ameya Kulkarni notifications@github.com wrote:
I am still getting the same error as @jpmam1 https://github.com/jpmam1 when trying to download other GTEx data, apart from the example (skin dataset). @jnpaulson https://github.com/jnpaulson is there an update with the work-around for this?
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Hi all, yes. Just decided on a workaround - and it will be implemented this coming week. I'll update this post soon.
Thank you
@DCGenomics , @ameya225 , @jpmam1
Hi all - apologies for the delay. As a temporary workaround (Bioconductor has a versioning delay) I'm placing the V6 data formatted already as a YARN processed ExpressionSet.
The file is an RDS object (meaning you read it in with the readRDS function). It's ~1.4 Gigs.
http://networkmedicine.org:3838/gtex_data/gtex_portal_normalized.rds
To grab it from the source within a script, one can easily:
library(downloader)
tmp = tempfile()
src = "http://networkmedicine.org:3838/gtex_data/gtex_portal_normalized.rds"
download(src,tmp)
obj = readRDS(tmp)
Hi there,
I was trying to run yarn on version 8 of GTEx. I changed the code for downloadGTEx to reflect the new websites for the new version. But I am getting a similar error has the previous people. Is there a workaround?
I've tried everything I could think of. It is still not working? Any suggestions? @jnpaulson
@DCGenomics , @ameya225 , @jpmam1
Hi all - apologies for the delay. As a temporary workaround (Bioconductor has a versioning delay) I'm placing the V6 data formatted already as a YARN processed ExpressionSet.
hi, question-related to the workaround: what is the normalized.rds file? normelized? raw counts? any filters made for selecting just part of the GTEx data?
thanks,
I failed at the first step. The example dataset (skin) worked great, but I wasn't able to load the GTEx data (failed on Mac and Ubuntu).
Any ideas on how to proceed would be very much appreciated.
Thanks, Jared