[BioC] heat maps

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Jun 14 18:23:43 CEST 2011


On Thu, Jun 9, 2011 at 4:44 PM, Brinsmade, Shaun R.
<Shaun.Brinsmade at tufts.edu> wrote:
> Hi All,
> This is not a Bioconductor question per se, but I was wondering if people have used the heatmap() function to create heatmaps of gene expression data. I would like to put a color key indicating changes in expression, but there is no apparent argument for "key". Alternatively, I believe that the gplots package contains an enhanced heatmap generator (heatmap.2) which does allow color keys to be made, but after downloading gplots, I tried to load the package and got the following:
> trying URL 'http://stat.ethz.ch/CRAN/bin/macosx/leopard/contrib/2.12/gplots_2.8.0.tgz'
> Content type 'application/x-tar' length 332781 bytes (324 Kb)
> opened URL
> ==================================================
> downloaded 324 Kb
> The downloaded packages are in
> /var/folders/Mg/Mgbv9bdKEqykYZ+cmG5adE+++TI/-Tmp-//RtmprvL7Vp/downloaded_packages
> Loading required package: gtools
> Error: package 'gtools' could not be loaded
> In addition: Warning message:
> In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
>  there is no package called 'gtools'
> Has anyone seen this problem before? If someone has an alternative method for generating a heat map from a .csv file, I'd love to know.

It's hard to tell what's going wrong since (i) it's not clear what you
did to get these messages (ie. you didn't show any code); and (ii) we
don't know what version/platform of R you have (ie. you should provide
the result of `sessionInfo()` when looking for help).

So please do that if the following doesn't help and you need more info.

If I just run:

R> install.packages('gplots')

>From an R session, everything works just fine. Is that what you tried
that leads to the errors you listed above?

What if you try to install each package that it depends on (ie.
gtools, gdata, and caTools) manually:

R> install.packages(c('gtools', 'gdata', 'caTools'))

Does that work?

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

More information about the Bioconductor mailing list