search

drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
Other
258 stars 98 forks source link

Something wrong with addHMRF #132

Closed BinDuan closed 1 year ago

BinDuan commented 3 years ago

I followed the tutorial "http://spatialgiotto.rc.fas.harvard.edu/giotto.visium.brain.html".

However, when I ran addHMRF, I got the warnings"FileNotFoundError: [Errno 2] No such file or directory: '11_HMRF/Spatial_genes/SG_topgenes_k20_scaled/result.spatial.zscore/k_20/ftest.beta.10.0.prob.txt'". I checked this file and there is indeed no this file.

I don't know why, can you give me some suggestions? Thanks

gcyuan commented 3 years ago

Hi

Sorry about the confusion, but the instruction at spatialgiotto.rc.harvard.edu is outdated. We are reconstructing our website, in the meantime, please refer to the website: github.com/RubD/Giotto_site for the up to date instructions. Please let us know if you continue to have any problem.

Best Guo-Cheng

On Sep 26, 2021, at 2:17 AM, BinDuan @.***> wrote:

 I followed the tutorial "http://spatialgiotto.rc.fas.harvard.edu/giotto.visium.brain.html".

However, when I ran addHMRF, I got the warnings"FileNotFoundError: [Errno 2] No such file or directory: '11_HMRF/Spatial_genes/SG_topgenes_k20_scaled/result.spatial.zscore/k_20/ftest.beta.10.0.prob.txt'". I checked this file and there is indeed no this file.

I don't know why, can you give me some suggestions? Thanks

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

bernard2012 commented 3 years ago

Are you trying to access a beta that you did not perform HMRF on? This may explain for lack of the file. Posting the full code might help to debug. Also try the Giotto docker image to see if the issue happens there. The Docker image gets rid of all environment related issues, so as to allow us focus on debugging the code.