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

[Maciej Jończyk]

Hi,

> Date: Mon, 27 Sep 2010 16:39:12 +0530
> From: Budhayash Gautam <budhayashgautam at gmail.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] how to save the expression values for two color data
> 	after	normalization
> Message-ID:
> 	<AANLkTik0d7ikiUnGB-dMkuimfur_CXqzhEBS0-ThJGWk at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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

You can export this data in following way:

1. Identify names of your columns, using rownames(dat2$M) and
rownames(dat2$A).

2. Next write code like this:
data_to_export=cbind(ID=dat$genes$ID *and the rest annotation columns in
similar way
,first_array_Mvalue=dat2$M[,1]
,first_array_Avalue=dat2$A[,1] *and so on, numbers in square-brackets
corresponds to order of your M and A values)

3. Export to tab-delimited file:
write.table(data_to_export,"path/file_name.txt",quote=FALSE,sep="\t")


Hope it helps,

>
> 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.
>
>
> --
> BUDHAYASH GAUTAM
> 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

Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1



___________________________________
NOCC, http://nocc.sourceforge.net