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statOmics / tradeSeqPaper

Scripts to reproduce analyses of tradeSeq paper.
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Have problem reproducing bulk RNA seq result #1

Closed wangxinge closed 4 years ago

wangxinge commented 4 years ago

Hi there,

I'm running the code for bulk RNA seq time course data. But my gamList is not a large list composed by each gene. So I cannot not proceed to look at fit for each gene.

fit GAM

gamList <- fitGAM(counts, pseudotime=time, cellWeights=weights, nknots=6)

May I ask do you know how to fix it?

koenvandenberge commented 4 years ago

We have changed the default behavior from tradeSeq to return a SingleCellExperiment object rather than a list of models, since it's more efficient. You can go back to having a list of models by setting sce=FALSE in the fitGAM function.

wangxinge commented 4 years ago

Thank you! It fixed my problem.