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uc-bd2k / GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator
https://shiny.ilincs.org/grein
GNU General Public License v2.0
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Header in downloadable data is partially worng #3

Closed kvittingseerup closed 6 years ago

kvittingseerup commented 6 years ago

I found this in the transcript level data (not sure about gene level data) The header looks like this:

",V1,Sample1,Sample2"

The data is structured as:

"rowNumber,transcriptId,Sample1"

This means that there is a headers missing - which will cause R's read.csv to skip the transcriptId column.

Is there a particular reason you would include rowNumbers in the data?

naimmahi commented 6 years ago

Hello @kvittingseerup, Thanks for your concern. Previously we didn't discard the row numbers from the data file and the sample names were in the form of SRR_GSM ids for the transcript level counts. But, we have changed it for both row names and GSM ids as well. The metadata, gene level counts, and transcript level counts should be matched now. Thanks.

kvittingseerup commented 6 years ago

I think an additional problem have been created as I can easily download count data - but when I try to download the transcript data it is not the right file name I get to download - and nothing is downloaded I just get a "Failed - server problem"

naimmahi commented 6 years ago

For which data set you're having this problem?

kvittingseerup commented 6 years ago

GSE77538

naimmahi commented 6 years ago

It should be good now.

kvittingseerup commented 6 years ago

Thanks for the fast fix - everything seems to be working now :-)