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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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runSCENIC_3_scoreCells error: columns not found #237

Open shexiaolu opened 2 years ago

shexiaolu commented 2 years ago

When i run runSCENIC_3_scoreCells with expression matrix, i met the following error: Using 12 cores. Catched error in AUCell_buildRankings() or in the histogram plot: column(s) not found: AAACGCTGTTGAGTCT_1..... AATTError in saveRDS(aucellRankings, file = getIntName(scenicOptions, "aucell_rankings")) : object 'aucellRankings' not found It seems like i lost some cells in the matrix, but i already checked the cells mentioned in the error message in the matrix and they did exist in the matrix. How can i fix this problem? Thank you for the contributions to SCENIC!

s-aibar commented 2 years ago

Dear @shexiaolu,

It is difficult to help you with the error without having access to the data itself, nor an example of reproducible code...

The easiest would be that you run this vignette: https://github.com/aertslab/SCENIC/blob/master/vignettes/detailedStep_3_scoreCells.Rmd You will probably be able to identify the problem then...

Please, let us know if it is indeed a problem with the code...

shexiaolu commented 2 years ago

Dear @shexiaolu,

It is difficult to help you with the error without having access to the data itself, nor an example of reproducible code...

The easiest would be that you run this vignette: https://github.com/aertslab/SCENIC/blob/master/vignettes/detailedStep_3_scoreCells.Rmd You will probably be able to identify the problem then...

Please, let us know if it is indeed a problem with the code...

Thanks for your answer! @s-aibar I followed the vignette step by step and everything went well except you didn't define the function regulonClusters which i found in other vignette. But when i ran runSCENIC_3_scoreCells again with the same prameters, i met another error:Error in signif(trhAssignment, 3) : non-numeric argument to mathematical function. What's more, sometimes there were no errors with the prameters. It is so strange and i can't figure out until now.