RunBLOBFISH: invalid 'times' argument

[GBeattie]

Hi,

Just getting to grips with this pipeline and I'm having an issue with RunBLOBFISH, see below for what I've done and the error, please let me know if I can provide any more information!

> fetalCNS <- ReadNetworks("GSE256493_Fetal_CNS_sorted_endothelial_cells_SCORPION.csv")
.'data.frame':	9584008 obs. of  3 variables:
 $ tf  : chr  "AHR" "AIRE" "ALX1" "ALX3" ...
 $ gene: chr  "A1BG" "A1BG" "A1BG" "A1BG" ...
 $ V3  : num  -0.57 -0.708 -0.68 -0.811 -0.849 ...
> head(pandas)
[1] -0.5325393 -0.3486638 -0.2189929 -0.2082745 -0.5899337 -0.3895899
> colnames(fetalCNS) <- c("tf", "gene", "score")
> str(setdiff(allGenes, unique(fetalCNS$gene)))
 chr [1:4] "HSPG" "GLYCAM1" "FASLG" "PDCD1LG2"
> fetalCNSSubnet <- RunBLOBFISH(geneSet = intersect(allGenes, fetalCNS$gene),
+                                networks = fetalCNS, alpha = 0.005, hopConstraint = 2, nullDistribution = pandas,
+                                verbose = TRUE)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': invalid 'times' argument

Thanks!
Gordon

[marouenbg]

Thanks Gordon! @taraeicher would you mind having a look at this?

[taraeicher]

@GBeattie Will you please send the input list of genes and the pandas file to teicher@hsph.harvard.edu? I'd like to try replicating this.

[taraeicher]

Note: We are currently waiting for @GBeattie to return from leave and confirm whether the issue is resolved. This appears to have been an issue with the input, not with the package.