[BioC] how to save the expression values for two color data after normalization

Budhayash Gautam budhayashgautam at gmail.com
Mon Sep 27 13:09:12 CEST 2010

Dear all

i am working on some smd data which is basically two color data. i
have normalize the data by the following command

> dat2<-normalizeWithinArrays(dat, method="loess","normexp", offset=50)

but as now i am trying to save its expression values by the following
command its is not giving any genes names with respect to rows without
which further analysis (annotation etc ) could not be done .

> dat.m<-dat2$M
> rownames(dat.m)<-dat2$genes$ProbeName
> write.table(dat.m, "tgondiiexpressionvalues.txt", sep="\t", row.names=T, col.names=T, quote=F)

and if i am trying ...

> rownames(dat.m) <-dat2$genes

following error is coming .....

Error in dimnames(x) <- dn :
  length of 'dimnames' [1] not equal to array extent

As i am very new to bioconductor and R problem may be very small but
for me it is too big......

thus please help me to solve this

please help me in the creation of proper matrix for the further analysis.

Assistant Professor
Department Of Computational Biology And Bioinformatics,
Jacob School of Biotechnology & Bioengineering (JSBB)
Sam Higginbottom Institute of Agriculture, Technology and Sciences
(SHIATS)- Deemed University, Naini, Allahabad.
U.P. 211007

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