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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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Error on runSCENIC_3_scoreCells #27

Closed galib36 closed 6 years ago

galib36 commented 6 years ago

I am getting the following error when I run runSCENIC_3_scoreCells, could you please tell me how to fix it.

runSCENIC_3_scoreCells(scenicOptions, exprMat_filtered) 22:36 Step 3. Analyzing the network activity in each individual cell

Number of regulons to evaluate on cells: 415 Biggest (non-extended) regulons: EGR1 (4140g) ELF1 (4100g) ATF3 (4088g) ETS2 (3401g) BCLAF1 (2974g) ETV6 (2873g) POLR2A (2530g) ETV5 (2436g) ELK3 (1792g) REL (1741g) Quantiles for the number of genes detected by cell: (Non-detected genes are shuffled at the end of the ranking.Keep in mind when choosing the threshold for calculating the AUC). min 1% 5% 10% 50% 100% 159.00 325.66 717.30 842.20 1863.00 5663.00 Using 2 cores. Using 2 cores. Error in sample.int(length(x), size, replace, prob) : cannot take a sample larger than the population when 'replace = FALSE'

s-aibar commented 6 years ago

The error is now fixed (sorry, I had not taken into account that some datasets might have fewer than 500 cells). If you re-install SCENIC package it should now work.