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pachterlab / sleuth

Differential analysis of RNA-Seq
http://pachterlab.github.io/sleuth
GNU General Public License v3.0
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Error in sleuth_live using gene_mode=TRUE #190

Closed lmigueel closed 4 years ago

lmigueel commented 6 years ago

Hello,

I got an error when I used the argument _genemode=TRUE on _sleuthlive. The first part of the figure shows a bug in gene box. When I tryed to find one gene, I got the error _"Error: could not find function "gene_fromgene" (second part of the figure). How I can solve this? Anyone can help me?

erro-sleuth_live

Thanks.

warrenmcg commented 6 years ago

Hi @lmigueel, thanks for pointing this out! This was a function that was supposed to be present that got lost in the shuffle of merging branches, and we didn't catch it during testing. I'm doing an emergency patch now.

warrenmcg commented 6 years ago

Hi @lmigueel, the issue is fixed. If you reinstall sleuth using devtools, the newest master commit should be installed, with the method restored.

devtools::install_github('pachterlab/sleuth')
lmigueel commented 6 years ago

Hi @warrenmcg,

Thanks for your reply. I reinstalled sleuth but I got one different error. Look the figure. It's seems that sleuth can not find the gene agregated column. The column _ensgene is on my transcript2gene file.

erro-leuth2

Regards,

warrenmcg commented 6 years ago

Hi @lmigueel, sorry you are continuing to have problems and thanks for bringing this back to our attention. I've identified the issue, and hopefully get a patch out soon.

warrenmcg commented 6 years ago

Hi @lmigueel, I've pushed a patch. If you want to immediately work with it before it gets folded into master, you can do so by doing the following:

devtools::github_install('warrenmcg/sleuth', ref = 'patch_g2g')

This is exactly the same version except with the patched included. Let me know if you experience any further difficulties. We'll close this issue when the patch gets folded into master

lmigueel commented 6 years ago

Hi @warrenmcg ,

I've tryed to plot again and still shows the same error _"Error in eval: object 'ensgene' not found".

I only installed from github, like you said, and start _sleuthlive. Do you think that is necessary run all script again? I mean _sleuthprep and _sleuthfit again?!

Thanks.

warrenmcg commented 6 years ago

@lmigueel, did you use the exact line that I gave you? This patch is not on master yet, so doing the usual install_github will result in no change and the same error. My patch works on my end, so it should work on yours.

lmigueel commented 6 years ago

Hello @warrenmcg ,

I would like to thank you. The bug is fixed.

Regards,