isa biclustering algorithm
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6.7 years ago
mannoulag1 ▴ 120

Hi, I need to do the isa biclustering algorithm on gene expression data matrix using ISA function of the Package ‘eisa’

library(eisa)
thr.gene <- 2.7 
 thr.cond <- 1.4 
 set.seed(1) # to get the same results, always 
 modules<- ISA(matrix, thr.gene=thr.gene, thr.cond=thr.cond)

but I have an error: impossible to find the ISA function ....

I do the isa biclustering from isa2 package and it is OK :

modules<-isa(normalized_matrix, thr.row=seq(1,3,by=0.5), thr.col=seq(1,3,by=0.5), no.seeds=100, direction=c("updown", "updown"))
    clusters<-isa.biclust(modules) # to convert the object with ISA modules to a Biclust object, so all the functions in the biclust package can be used on it.

But I read in the tutorial : If you analyze gene expression data, then we suggest using the interface provided in the eisa package. For other data, use the isa2 package directly.

how to obtain the modules using eisa package? thank you

isa biclustering gene expression data R eisa • 1.2k views
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