Hi Vincent, thanks for your reply.

Here you have the sessionInfo()

> sessionInfo()
R version 2.13.0 Patched (2011-04-21 r55576)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
  [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252    LC_MONETARY=English_United States.1252
LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
  [1] stats     graphics  grDevices datasets  utils     methods   base
other attached packages:
  [1] hgu95av2cdf_2.8.0   affydata_1.11.11    affyQCReport_1.30.0
lattice_0.19-26     affy_1.30.0         Biobase_2.12.1
rcom_2.2-3.1        rscproxy_1.3-1
loaded via a namespace (and not attached):
  [1] affyio_1.20.0         affyPLM_1.28.5        annotate_1.30.0
AnnotationDbi_1.14.1  Biostrings_2.20.0     Cairo_1.4-9
cluster_1.13.3        DBI_0.2-5             gcrma_2.24.1
[10] genefilter_1.34.0     grid_2.13.0           Hmisc_3.8-3
hwriter_1.3           IRanges_1.10.0        latticeExtra_0.6-14
preprocessCore_1.14.0 RColorBrewer_1.0-2    RSQLite_0.9-4
[19] setRNG_2009.11-1      simpleaffy_2.28.0     splines_2.13.0
survival_2.36-9       tools_2.13.0          xtable_1.5-6


By the way, when I use the affyQCreport for a quality check the empirical
density for the log intensity is plotted nicely.

Maybe it helps to know that my R installation is from a bundle named
RAndFriends (http://rcom.univie.ac.at/) which include a COM server to
comunicate with applications like Excel and Matlab.
I look forward to hear from you.

Omar



On Wed, May 4, 2011 at 6:45 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote:

> what is your sessionInfo()?
>
>   On Wed, May 4, 2011 at 7:39 AM, Omar Gutierrez Arenas <
> tardebut@gmail.com> wrote:
>
>> Dear Colleagues,
>>
>> I have been trying to run some of the examples described in the affy prime
>> vignette and I'm having problems with image() and hist().
>>
>> For example,
>>
>>  > require(affy)
>>
>> > require(affydata)
>>
>> > data(Dilution)
>>
>> > Dilution
>> trying URL '
>>
>> http://bioconductor.org/packages/2.8/data/annotation/bin/windows/contrib/2.13/hgu95av2cdf_2.8.0.zip
>> '
>> Content type 'application/zip' length 1343719 bytes (1.3 Mb)
>> opened URL
>> downloaded 1.3 Mb
>> package 'hgu95av2cdf' successfully unpacked and MD5 sums checked
>> The downloaded packages are in
>>        C:\Users\Omar\AppData\Local\Temp\Rtmpeah9J5\downloaded_packages
>> Attaching package: 'hgu95av2cdf'
>> The following object(s) are masked from 'package:mouse4302cdf':
>>    i2xy, xy2i
>> AffyBatch object
>> size of arrays=640x640 features (27212 kb)
>> cdf=HG_U95Av2 (12625 affyids)
>> number of samples=4
>> number of genes=12625
>> annotation=hgu95av2
>> notes=
>> Now, following the vignette I try,
>>
>> > image(Dilution)
>> Error in image.default(Dilution) : 'z' must be a matrix
>>
>>
> this call should not be invoking image.default, but rather affy::image ...
> your searchlist is messed up, or you
> have failed to do library(affy)
>
>
>> and then,
>>
>> > hist(Dilution[, 1:2])
>> Error in hist.default(Dilution[, 1:2]) : 'x' must be numeric
>>
>> However, the following works,
>>
>> plotDensity(exprs(Dilution), log="x")
>>
>> but the curve is not smooth at all.
>>
>> Other examples from the same vignette can be run with no problems.
>>
>> Am I missing something here? I tried the vignette examples because my own
>> data was having problems with this functions.
>>
>> My OS is Windows 7 with R 2.13 and Bioconductor 2.8.
>>
>> I look forward to hear from some of you.
>>
>> Thanks in advance,
>>
>> Omar
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
>

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