Error in quantile.default(corGSM_MM$maxDelta, 0.75):: missing values and NaN's not allowed if 'na.rm' is FALSE

GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

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Error in quantile.default(corGSM_MM$maxDelta, 0.75):: missing values and NaN's not allowed if 'na.rm' is FALSE #604

Closed sylestiel closed 3 years ago

sylestiel commented 3 years ago

Problem encountered when running scripts from Chapter15.4.2 Step 2. Identify Correlated TF Motifs and TF Gene Score/Expression on Multiomic ATAC+GEX data.

Screen shot or error:

ArchR Log: ArchR-correlateMatrices-5997523071c7-Date-2021-03-08_Time-14-28-13.log

Session Info:

ldorozco commented 3 years ago

I ran into a similar error message for a different step analyzing multi-omics data, and the following filter fixed that error. It might work for you. It is from the "Ex-Analyze-Multiome" tutorial:

proj <- proj[ !is.na(proj$Gex_nUMI)]

sylestiel commented 3 years ago

Thanks @ldorozco

Can you tell me rather where to incorporate this into the above mentioned script? Thanks!

sylestiel commented 3 years ago

Fixed by setting na.rm=TRUE