Hi everyone.
One of the datasets has a malformed Ensembl gene expression file. Please hold of on making submissions if you are using the Ensembl files until this is fixed.
Thanks!
Created by Andrew Lamb andrewelamb Yes, it looks like you were correct, the fine-grained data wasn't updated as well. I've gone ahead and updated them. I had succesful submissions in the coarse-grain challenge but kept failing in the fine-grained.
After debugging I found that the problem is still there:
Also there is an empty rowname, which makes my submission crash.
```
[1] "input/DS389-ensg-gene-expr.csv"
[1] "Gene
[2] ""
[3] "---"
[4] "ENSG00000000003 /// OTTHUMG00000022002"
[5] "ENSG00000000005 /// OTTHUMG00000022001"
```
If you can fix this one too that would be great! Thanks! Thanks for your responce. In the log file also the part that utilizes Ensembl ids says that 'Total of 2.24 % genes are found', which sounds like there is something going on with them as well (in other datasets the proportion is a lot higher). However, if the issue is resolved already, the odds are that I have made some mistakes, I'll keep debugging. @maja
The issues should be resolved with both queues.
I'm looking at your logs, and without giving away too much of your method, it looks like your last 3 fine-grained submissions are having issues with Entrez genes, not Ensembl. Hi Maria,
On September 1, the problem was there also on the fine grained challenge.
Cheers,
Jean-Marie Hi,
Is there any chance that similar issue is still present in some Subchallenge 2 data (my code crashes on one of them)?
Thanks,
Maria @maja
I've just made the gene name fix. Okay, thanks for leting me know!
BR,
Maria Hi Maria,
Yesterday (September 1) the problem was still there.
Cheers,
Jean-Marie Has this issue been solved (i.e. is it safe to submit if I utilize the Ensembl data)?
Thanks!
- Maria