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drlaguna / GMSCA

GMSCA: Gene Multifunctionality in Secondary Co-expression Analysis
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Error GPCNA::removePrimaryEffect #1

Closed juanbot closed 5 years ago

juanbot commented 5 years ago

Hi, when I do this

GPCNA::removePrimaryEffect( expr.data =selectData("AMYLOID"), target.enrichment = c("A", "B"), net = readRDS("~/Dropbox/collab/dervis/bootstrap/netBootAMYLOID_boot.13.it.30.b.30.rds"))

I get this [1] 58 19328 Error in [<-(*tmp*, , i, value = is.element(geneAll, geneIn[labelIn == : subscript out of bounds

selectData returns a data.frame with genes in columns and samples in rows. I think it would be good if this method GPCNA::removePrimaryEffect does some preliminary checks on the parameters (e.g. do we have the target enrichment labels in the set??, is the network of the right format?)

juanbot commented 5 years ago

It doesn´t work neither with correct target.enrichment values as in

GPCNA::removePrimaryEffect( expr.data =selectData("AMYLOID"), target.enrichment = c("Interneuron"), net = readRDS("~/Dropbox/collab/dervis/bootstrap/netBootAMYLOID_boot.13.it.30.b.30.rds")) [1] 58 19328 Error in [<-(*tmp*, , i, value = is.element(geneAll, geneIn[labelIn == : subscript out of bounds