Error in fitGAM: can't correct step size

statOmics / tradeSeq

TRAjectory-based Differential Expression analysis for SEQuencing data

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Error in fitGAM: can't correct step size #53

Closed dakotakatz closed 4 years ago

dakotakatz commented 4 years ago

Hi,

I am trying to run the fitGAM function on SlingshotDataSet and I keep getting the error:

Screen Shot 2020-05-29 at 10 19 58 AM

When I tried running it by extracting the pseudotime and cellWeights from a SingleCellExperiment instead, I got an error that the pseudotime had NA values even though I had set na = FALSE in slingPseudotime.

Do you have any idea what is causing this error?

koenvandenberge commented 4 years ago

Hi,

Thank you for your interest in using tradeSeq. This is an mgcv error which we did not catch, but we should have fixed that in recent versions of tradeSeq. Could you please try re-installing the latest version of tradeSeq from GitHub and check whether the error persists?

HectorRDB commented 4 years ago

Closed after #57