buildSignatureMatrixMAST does not finish

[favilaco]

Dear Daphne Tsoucas,

I am trying to run the example mentioned in the vignette with the files "dataSC.RData","dataBulk.RData" and "labels.RData".

Everything seems to be running fine but in the end the "Signature" object is not created (apparently "results/CycISC_lrTest.csv" is not being created...).

Would it be possible to look into this? Thanks a million!

This is the log:

[1] "finished log2"
[1] "CycISC"
[1] "finished cells.symbol.list2"
[1] "finished cells.coord.list2"
[1] "finished cells.symbol.list1"
[1] "finished cells.coord.list1"
[1] "finished data.used.log2.ordered"
[1] "finished group.v"
[1] "finished log2.stat.result"
[1] "finished m.auc"
[1] "finished bigtable"
[1] "finished filter bigtable by log2fc"
[1] "finished filter data.1"
[1] "finished filter data.2"
[1] "finished get log2fold_change"
[1] "finished get counts"
[1] "finished get groups"
No id variables; using all as measure variables
[1] "finished get data_for_MIST"
Assuming data assay in position 1, with name Et is log-transformed.
[1] "finished get FromFlatDF"
[1] "finished get subset"
 Completed [-------------------------------------------------]   1% with 0 failures Completed [>------------------------------------------------]   1% with 0 failures Completed [>------------------------------------------------]   2% with 0 failures
...
Completed [=================================================] 100% with 0 failures                                                                                   
Done!
Fitted zlm on 1388 genes and 3000 cells.
 Using BayesGLMlike ~ Population 
Refitting on reduced model...
 Completed [>------------------------------------------------]   1% with 0 failures Completed [>------------------------------------------------]   2% with 0 failures Completed [>------------------------------------------------]   3% with 0 failures Completed [=>-----------------------------------------------]   3% with 0 failures 
...
Completed [=================================================] 100% with 0 failures                                                                                   
Done!
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning messages:
1: 'zlm.SingleCellAssay' is deprecated.
Use 'zlm' instead.
See help("Deprecated") 
2: In file(file, ifelse(append, "a", "w")) :
  cannot open file 'results/CycISC_lrTest.csv': No such file or directory

Kind regards,
Francisco

[favilaco]

Never mind, I just found out it was a permission issue inside the folder... apologies for the inconvenience!

Solved! :)