search

Katsevich-Lab / sceptre

An R package for single-cell CRISPR screen data analysis emphasizing statistical rigor, massive scalability, and ease of use.
https://katsevich-lab.github.io/sceptre/
GNU General Public License v3.0
26 stars 8 forks source link

Two or more non-targeting gRNAs must be present when running a calibration check. #41

Closed redbybeing closed 1 year ago

redbybeing commented 1 year ago

Hello,

I have another question..

I get this message when I try to run calibration check with run_sceptre_highmoi_experimental

Error in check_inputs(response_matrix, grna_matrix, covariate_data_frame,  : 
  Two or more non-targeting gRNAs must be present when running a calibration check. gRNAs that are non-targeting should be assigned a gRNA group label of 'non-targeting'.

Unfortunately, in my library, I only have one single gRNA (guide-GFP) as a non-targeting gRNA. All others are gene targeting gRNAs. I didn't know that it's better to include multiple non-targeting gRNAs when I first generated the library. In this case, what is the best action I can take to run sceptre new high-moi with my current data? Skip calibration and run discovery?

I recall that in previous high-moi scepter, it didn't matter if I only had one single non-targeting gRNA, because I was able to define my own negative control pairs with just one non-targeting gRNA (GFPguide vs all genes).

ekatsevi commented 1 year ago

Hi Jiseok, I think this may be a bug; you should still be able to carry out a calibration check in high-MOI with just one gRNA. I'll let @timothy-barry address this further.

timothy-barry commented 1 year ago

The package no longer throws this error.