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
>
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>
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