Entering edit mode
3.7 years ago
roysense
•
0
#package upload
library(cmapR)
#object creation
g<-GCT()
gct_file<-system.file("extdata","PAAD_new.gct",package="cmapR")
(g<-GCT(src=gct_file))
class(g)
#matrix Extraction m
m<-mat(g)
#column and row metadata extraction
rdesc<-meta(g,dimension="row")
cdesc<-meta(g,dimension="column")
#column and row id extraction
rid<-ids(g,dimension="row")
cid<-ids(g,dimension="column")
#Before using pcaExplorer we need two important files, the matrix file and the cdesc file
write_tbl(m,"m.txt")
write_tbl(cdesc,"cdesc.txt")
#But we can directly attach the files to pcaExplorer
library(pcaExplorer)
pcaExplorer(countmatrix = m, coldata = cdesc)
In the pcaExplorer webpage, i pressed the generate dds and dst object and the screen greyed out
In the R console I am seeing Listening on http://127.0.0.1:6363
Warning: Error in DESeqDataSet: some values in assay are negative
[No stack trace available]
Warning: Error in DESeqDataSet: some values in assay are negative
[No stack trace available]
Or should I remove negative values from the matrix?? But, if I do that will my results change?
P:S- All NaN values are already removed
Stars, Please help.
What is the output of: