Thanks a lot for the help. It works fine now.

Wei

On Mon, Mar 16, 2009 at 12:25 PM, Saroj K Mohapatra <smohapat@vbi.vt.edu>wrote:

> Hi Wei,
>
> I think you need to set the row.names argument in read.csv to 1.
>
> > ?read.csv
> -----------------------
> row.names: a vector of row names.  This can be a vector giving the
>          actual row names, or a single number giving the column of the
>          table which contains the row names, or character string
>          giving the name of the table column containing the row names.
>
>          If there is a header and the first row contains one fewer
>          field than the number of columns, the first column in the
>          input is used for the row names.  Otherwise if 'row.names' is
>          missing, the rows are numbered.
>
>          Using 'row.names = NULL' forces row numbering. Missing or
>          'NULL' 'row.names' generate row names that are considered to
>          be 'automatic' (and not preserved by 'as.matrix').
> -----------------------
>
> Because the row.names are missing from your command, the rows were numbered
> automatically (see above).
>
> If you call:
> >  data=read.csv("file.csv", header=T, row.names=1)
>
> it would automatically read the row labels which should show as expected on
> the heatmap. I hope that solves this problem.
>
> Best,
> Saroj
>
> ----- Original Message -----
> From: "Christof Winter" <winter@biotec.tu-dresden.de>
> To: bioconductor@stat.math.ethz.ch
> Cc: public-bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7@ciao.gmane.org
> Sent: Monday, March 16, 2009 12:15:53 PM GMT -05:00 US/Canada Eastern
> Subject: Re: [BioC] question about heatmap.2
>
> Wei Xu wrote, On 16.03.2009 16:52:
> > Hi, there,
> >
> > This is a simple question.
> >
> > I'm trying to read my data from a .csv file and draw a heatmap with
> > heatmap.2.
> > Here is my code,
> >
> > data=read.csv("file.csv", header=T)
> > x=as.matrix(data[,2:5])
> > heatmap.2(x)
> >
> > The file.csv includes 5 columns and 118 rows. First columns are the
> labels
> > for the each probe.
> >
> >               ID Temperature Agitation Oxygen Adhesion
> > BG03_B01      -0.098     0.013  0.007    0.064
> > BG04_A09       0.025     0.013 -0.011   -0.054
> > BG04_A11      -0.005     0.000  0.018    0.050
> >
> > When I had my heatmap, the probes were labeled with the number from 1 to
> 117
> > instead of the ID numbers in the file. My question is how can I label
> each
> > probe in the heatmap with their IDs. Thanks.
> >
> > Wei
> >
>
> Try
>
> heatmap.2(x, labRow=x$ID)
>
> Christof
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> Computational Biology
> VBI @ Virginia Tech
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>


-- 
Wei Xu
Aquatic Animal Health Laboratory
Pathobiology and Diagnostic Investigation
College of Veterinary Medicine
Michigan State University
East Lansing, MI, 48824
Tel: 1-517-432-8258

	[[alternative HTML version deleted]]

