Open salbrec opened 2 years ago
Hi Steffen, SCALE has been updated for supporting scanpy that all results are saved in h5ad format file. You should find the binary imputed output in adata.obsm['binary'] after reading the output file adata.h5ad using read_h5ad function in scanpy. Lei
Hi Lei, thanks for the quick reply! The h5ad format was new to me, however, it was straight forward to get the "binary". As far as I could see, the "impute" output is also there, even though I didn't use the --impute flag. After the update, are those imputation flags true by default? Thanks again, Steffen
Hi Steffen, the 'binary' is obtained after calculating the 'impute' in SCALE, I can del 'impute' if you don't need it. To get a 'binary' without 'impute', you just need to git clone the newest rep and install it again (not via pip). Lei
Dear Lei, I recently encountered a problem regarding the imputation. I used SCALE already some time ago and I remember I could get data about imputation using the --binary flag (basically I don't need numerical imputed data) which was working back then. However, when I ran SCALE yesterday, I got no imputed output. Everything else seems to be just fine, just the "binary_imputed" folder is missing. More information can be taken from the picture I added. Might be also important: When I first used SCALE it was (I guess) still in the year of publication and in the meanwhile I pulled the most recent version. Can you please check if there is a bug or a wrong usage from my side? Thanks in advance! Steffen