Hi again,

Sorry for the misunderstanding.

I have repeated what you have done and got the same issue. See below:

 > library(affyQCReport)
 > library(affydata)
 > data(Dilution)
 > QCReport(Dilution,file='qc.pdf')
Error in as.double(y) :
   cannot coerce type 'S4' to vector of type 'double'
 > sessionInfo()

R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hgu95av2cdf_2.7.0   affydata_1.11.10    affyQCReport_1.28.0  
lattice_0.19-13
[5] affy_1.28.0         Biobase_2.10.0

loaded via a namespace (and not attached):
  [1] affyio_1.18.0         affyPLM_1.26.0        annotate_1.28.0
  [4] AnnotationDbi_1.12.0  Biostrings_2.18.2     DBI_0.2-5
  [7] gcrma_2.22.0          genefilter_1.32.0     grid_2.12.0
[10] IRanges_1.8.0         preprocessCore_1.12.0 RColorBrewer_1.0-2
[13] RSQLite_0.9-2         simpleaffy_2.26.0     splines_2.12.0
[16] survival_2.35-8       tools_2.12.0          xtable_1.5-6

Lorenzo

On 1 Dec 2010, at 11:40, Sean Davis wrote:

>
>
> On Wed, Dec 1, 2010 at 6:23 AM, Lorenzo Melchor <lorenzo.melchor@icr.ac.uk 
> > wrote:
> Hi, Sean.
>
> Please, find attached one or the examples that I have tried to run.  
> The problem is regardless of the samples you work with.
>
>
> Hi, Lorenzo.  If I run the example for QCReport, I see the same error.
>
> Here is what I meant with reproducible example and sessionInfo().
>
> > library(affyQCReport)
> > library(affydata)
> > data(Dilution)
> > QCReport(Dilution,file='qc.pdf')
> Error in as.double(y) :
>   cannot coerce type 'S4' to vector of type 'double'
> > sessionInfo()
> R version 2.12.0 Under development (unstable) (2010-04-30 r51866)
> i386-apple-darwin9.8.0
>
> locale:
> [1] en_US/en_US/C/C/en_US/en_US
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] hgu95av2cdf_2.7.0   affydata_1.11.10    affyQCReport_1.28.0
> [4] lattice_0.18-8      affy_1.27.0         Biobase_2.10.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.17.0         affyPLM_1.26.0        annotate_1.27.0
>  [4] AnnotationDbi_1.11.9  Biostrings_2.17.8     DBI_0.2-5
>  [7] gcrma_2.22.0          genefilter_1.31.0     grid_2.12.0
> [10] IRanges_1.7.7         preprocessCore_1.11.0 RColorBrewer_1.0-2
> [13] RSQLite_0.9-2         simpleaffy_2.26.0     splines_2.12.0
> [16] survival_2.35-8       tools_2.12.0          xtable_1.5-6
>
>
>
>
> On 1 Dec 2010, at 11:17, Sean Davis wrote:
>
>
>
> On Wed, Dec 1, 2010 at 5:59 AM, Lorenzo Melchor <lorenzo.melchor@icr.ac.uk 
> > wrote:
> Hi there,
>
> I have been trying to use AffyQCReport for a few days now and I keep
> having the same problem again and again.
>
> I load the package with the usual library(affy) and
> library(affyQCReport) commands, so I type then the next command
> obtaining an error as a result.
>
>  > QCReport(test,file="qualityReport.pdf")
>
> Error in as.double(y) :
>  cannot coerce type 'S4' to vector of type 'double'
>
> When checking in my working directory, I find a pdf file with only the
> first two pages of any AffyQCReport.
>
> It seems odd because some other people at my centre has tried to do
> the same analysis, and got the same error.
>
> Would you know which the cause would be?
>
>
> Hi, Lorenzo.
>
> Can you give a reproducible example and sessionInfo()?
>
> Sean
>
> Lorenzo Melchor, PhD
> Mammary Stem Cell Team
> The Breakthrough Breast Cancer Research Centre (ICR)
> 237 Fulham Road
> SW3 6JB
> lorenzo.melchor@icr.ac.uk
>
>
>
>
>
> The Institute of Cancer Research: Royal Cancer Hospital, a  
> charitable Company Limited by Guarantee, Registered in England under  
> Company No. 534147 with its Registered Office at 123 Old Brompton  
> Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the...{{dropped:29}}

