Thanks, James. The problem is fixed. Some of the packages in gplots are
missing. Manually installation in needed in my system...

Wei


On Thu, Feb 20, 2014 at 2:49 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Wei,
>
> First, gplots is a CRAN package so you should be asking about this on
> R-help, not Bioc-help.
>
> However, you might try re-installing, as the function is definitely there:
>
> > library(gplots)
> KernSmooth 2.23 loaded
> Copyright M. P. Wand 1997-2009
>
> Attaching package: 'gplots'
>
> The following object is masked from 'package:stats':
>
> lowess
>
> > args(heatmap.2)
> function (x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE,
> distfun = dist, hclustfun = hclust, dendrogram = c("both",
> "row", "column", "none"), symm = FALSE, scale = c("none",
> "row", "column"), na.rm = TRUE, revC = identical(Colv,
> "Rowv"), add.expr, breaks, symbreaks = min(x < 0, na.rm = TRUE) ||
> scale != "none", col = "heat.colors", colsep, rowsep,
> sepcolor = "white", sepwidth = c(0.05, 0.05), cellnote, notecex = 1,
> notecol = "cyan", na.color = par("bg"), trace = c("column",
> "row", "both", "none"), tracecol = "cyan", hline = median(breaks),
> vline = median(breaks), linecol = tracecol, margins = c(5,
> 5), ColSideColors, RowSideColors, cexRow = 0.2 + 1/log10(nr),
> cexCol = 0.2 + 1/log10(nc), labRow = NULL, labCol = NULL,
> srtRow = NULL, srtCol = NULL, adjRow = c(0, NA), adjCol = c(NA,
> 0), offsetRow = 0.5, offsetCol = 0.5, key = TRUE, keysize = 1.5,
> density.info = c("histogram", "density", "none"), denscol = tracecol,
> symkey = min(x < 0, na.rm = TRUE) || symbreaks, densadj = 0.25,
> main = NULL, xlab = NULL, ylab = NULL, lmat = NULL, lhei = NULL,
> lwid = NULL, ...)
> NULL
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] gplots_2.12.1
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-6 caTools_1.16 gdata_2.13.2 gtools_3.3.0
> [5] KernSmooth_2.23-10
>
> Best,
>
> Jim
>
>
>
>
> On 2/20/2014 3:42 PM, Wei Xu wrote:
>
>> Hi,
>>
>> This is probably not common but after I update R tp 3.0.2, the heatmap.2
>> cannot be found in gplots. I'm sure that I loaded the gplots already but
>> whenever I tried heatmap.2, I was told that this function cannot be found.
>> It didn't seem to be reported in this list so I guess it's just my
>> problem.
>> Thanks.
>>
>> Wei
>>
>>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>


-- 
Wei Xu, Ph.D.

Wound Healing and Regenerative Medicine Laboratory
Department of Surgery / Plastic Surgery Division
Northwestern University, Feinberg School of Medicine
303 East Chicago Ave, Tarry 4-720
Chicago, IL 60611
Phone: (312) 908 0566
Fax: (312) 908 4013

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