[BioC] Error coerce in AffyQCReport

[Martin Morgan]

On 12/01/2010 03:51 AM, Lorenzo Melchor wrote:
> 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'

The arrayQualityMetrics library might be a good alternative. Martin

>  > 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 at 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 at 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 at 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}}
> 
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