single cell differential expression analyses

Question

[bioinformatics]

Hi,

I'm working through chapter 7 of this book: http://bioconductor.org/books/3.14/OSCA.multisample/human-pbmcs-10x-genomics.html#human-pbmcs-10x-genomics.

For 7.2 data loading I have used this command (mat, mat1, mat2, mat3, mat4, mat5 are each count matrix's with gene names and barcodes)

all.sce <- list(mat=TENxPBMCData('pbmc3k'),mat1=TENxPBMCData('pbmc4k'),mat2=TENxPBMCData('pbmc33k'), mat3=TENxPBMCData('pbmc68k'), mat4=TENxPBMCData('frozen_pbmc_donor_a'),mat5=TENxPBMCData('pbmc6k'),)

However I get the following error message:

error in list(mat = TENxPBMCData("pbmc3k"), mat1 = TENxPBMCData("pbmc4k"),  : 
  argument 7 is empty

Does anyone know where I have gone wrong?

Thank you

Answer 1

[Eijy Nagai]

Hi,

Would it be because you left a comma after the "mat5=TENxPBMCData('pbmc6k')"?

Best regards,

Eijy

[bioinformatics]

I removed the comma and the command worked.

Thankyou for your suggestion.

[Eijy Nagai]

You're welcome! Good luck!