Pseudotime analysis on bulk RNASeq using monocle
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pbachali ▴ 20
Last seen 3.0 years ago

Hi All, I am trying to do some trajectory analysis on bulk RNAseq data. I have a expression data in gene by sample matrix along with phenodata and the featureData. I am trying to use monocle in R to perform some pseudotime analysis. I know that monocle is meant for single cell RNASeq data. I am trying to see if I can run on bulk RNASeq data. I am able to create newCellSDataSet object. But I am stuck at dimensionality reduction step. It is throwing me the following error.

Error in if (cds@expressionFamily@vfamily %in% c("negbinomial", "negbinomial.size")) { : argument is of length zero

Does it has to do the experiment type (like SIngleCellRNAseq or Bulk RNAseq)? I don't know how to proceed further.![enter image description here][1]

pseudotime monocle dimensionality • 1.3k views
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What trajectory would you expect to see? Trajectory of your samples? But then that would only be possible if you have hundreds/thousands of samples.


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