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

[Budhayash Gautam]

hello everyone

lots of thanks to all of u to help me by giving Ur precious suggestions.


On Mon, Sep 27, 2010 at 4:39 PM, Budhayash Gautam
<budhayashgautam at gmail.com> wrote:
> 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.
>
>
> --
> 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
>



-- 
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