R help - Jul 2011 - heatmap with RNA-Seq data

Hi all,
new to this forum
I'm try to using R to draw a heatmap of my RNA-seq data
before doing that I did a log2 transformation of my data and produce a lot
-inf in the matrix 
when I try to use the heatmap function, it seems can not deal with the -inf
so I was wondering how to deal with these gene with 0rpkm(they are not 0 in
all samples, so I want to keep them in the heatmap)
thanks

--
View this message in context:
http://r.789695.n4.nabble.com/heatmap-with-RNA-Seq-data-tp3676207p3676207.html
Sent from the R help mailing list archive at Nabble.com.

On Jul 18, 2011, at 3:34 PM, rebioman wrote:
> Hi all,
> new to this forum
> I'm try to using R to draw a heatmap of my RNA-seq data
> before doing that I did a log2 transformation of my data and produce  
> a lot
> -inf in the matrix
> when I try to use the heatmap function, it seems can not deal with  
> the -inf
> so I was wondering how to deal with these gene with 0rpkm(they are  
> not 0 in
> all samples, so I want to keep them in the heatmap)
> thanks
?is.infinite

Could be used to replace infinities with a suitably low number, which  
can only be determined from the data context.
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/heatmap-with-RNA-Seq-data-tp3676207p3676207.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT