not-yet-implemented 'Matrix' subsetting

hmassalha commented 4 years ago

Hi, I am running the pipeline as in the website @pimentel https://bustools.github.io/BUS_notebooks_R/velocity.html using my data. I am getting the following error:

seu <- CreateSeuratObject(uf, assay = "uf") %>% SCTransform(assay = "uf", new.assay.name = "spliced")
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Calculating cell attributes for input UMI matrix
Error in umi[genes, ] :
  invalid or not-yet-implemented 'Matrix' subsetting

When I ran the two lines separately I fount the error caused by SCTransform(seu, ,assay = "uf", new.assay.name = "spliced") command.

Any help? any hint? I looked on the web and didn't found any critical explanation of why getting this error! It seems a Seuart error, hopefully, you have any suggestion on how to prepare the data to create the Seurat obj.

Many thanks, HM

stefanonard85 commented 4 years ago

I am getting the same error

sweebinee commented 3 years ago

Did you guys solve the problem? I've got the same error.

pachterlab / kallisto

not-yet-implemented 'Matrix' subsetting #238