Dear All,

 

Is it possible to export transformed data from the lumi package? I want to
use the data in another statistical program and export it from R as an .txt
file. I've tried write.table command but it does not work on batch objects.
I could export expression values by using temp <- exprs(lumi.T) but the file
does not include gene names.

 

The data I want to export has been produced like this (lumi version 1.10.2):

 

smctarget <- 'H:/Geeniekspressio/Illumina_files/targetidsmc.txt'

smctarget.lumi <- lumiR(smctarget, detectionTh=0.01, QC=TRUE,
inputAnnotation=FALSE, checkDupId=FALSE, lib='lumiHumanAll')

lumi.T <- lumiT(smctarget.lumi, method=c('log2'), ifPlot=TRUE)

 

or with a command used to normalize the first data: 

lumiqtlog2.N <- lumiN(lumi.T, method='quantile', verbose=TRUE)

 

What I would like to export is expression values from the object lumi.T or
lumigtlog2.N. I would like the data to include the targetID names and the
expression values after transformation or after transformation+normalization
from each of the chips in the data.

 

Could anybody help? Are there help pages available which address this issue?

 

-Mervi

 


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