Cannot find "PulseSeq_UMI_counts.rds"

adamh-broad / single_cell_airway

R code for single-cell analysis of airway epithelial cells

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Cannot find "PulseSeq_UMI_counts.rds" #2

Open csbl-usp opened 5 years ago

csbl-usp commented 5 years ago

Hello,

Great article, and very good practice to put the underlying code online in .Rmd.

I could not find the .rds file "ps_umis = readRDS("PulseSeq_UMI_counts.rds")" that is read to the ps_umis in the PulseSeq.Rmd file and I am not able to create the ps Seurat object.

Am I missing something or is it actually missing in the repo?

Thanks for the time,

Tiago

adamh-broad commented 5 years ago

Hey Tiago, Thanks! I updated the .Rmd to more clearly show how to grab that .rds file from the GEO accession. Let me know if you have questions

Best, Adam

BarbaraFFonseca commented 3 years ago

Hello Adam and great article!

Just for info, in the updated .Rmd the code tries to grab the file in a wrong GEO number. The right one I think it is GSE103354, as written in the not updated file... Sorry to bother you with this and thank you again for the code on .Rmd ! Best Barbara