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AllenInstitute / scrattch.mapping

Genearlized mapping scripts for RNA-seq and Patch-seq data
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standard deviation is zero Warning #9

Closed scseeman closed 1 year ago

scseeman commented 1 year ago

Using correlation mapping on a subset of the original MERSCOPE dataset I received the following warning. Mapping completed and results seemed ok.

[1] "Correlation-based mapping" Warning message: In cor(as.matrix(test.dat), cl.dat) : the standard deviation is zero

jeremymiller commented 1 year ago

I think you can ignore this warning. For me this often happens with sparse data (e.g., if there is exactly 1 non-zero value). It may mean that for some cells the correlation will be unreliable, but if the data is that sparse, then ANY method for mapping is unreliable. If your data is NOT sparse, then let's leave this issue open.

From: Stephanie Seeman @.> Sent: Wednesday, March 29, 2023 10:52 AM To: AllenInstitute/scrattch-mapping @.> Cc: Subscribed @.***> Subject: [AllenInstitute/scrattch-mapping] standard deviation is zero Warning (Issue #9)

Using correlation mapping on a subset of the original MERSCOPE dataset I received the following warning. Mapping completed and results seemed ok.

[1] "Correlation-based mapping" Warning message: In cor(as.matrix(test.dat), cl.dat) : the standard deviation is zero

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scseeman commented 1 year ago

ok, I think this would be considered "sparse", it's only 60 genes. I'll close