[BioC] readQpcrBatch()

[Valerie Obenchain]

John,

It looks like one of the files in your directory is not properly 
formatted. See ?readQpcr (readQpcrBatch just calls readQpcr for each 
file). The function is expecting the first column to be gene/primer 
pairs, the second to be plate indices of each pari and the remaining 
columns are Ct values. The primerNames error you are seeing below 
pertains to the first column.

To find the offending file you could try a loop with readQpcr on each file.

Valerie


On 06/01/11 03:57, John Coulthard wrote:
> Dear list
>
> Using the qpcrNorm package I can read single data files into R with readQpcr() but when I try to read in multiple files with readQpcrBatch() I'm getting an error and I don't understand what it's trying to tell me. Please see below.
>
> Many thanks
> John
>
>
> [john at y90-w-d RAT]$ R --vanilla
>
> R version 2.13.0 (2011-04-13)
> Copyright (C) 2011 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: i386-redhat-linux-gnu (32-bit)
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>    Natural language support but running in an English locale
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>    
>> library(qpcrNorm)
>>      
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>    Vignettes contain introductory material. To view, type
>    'openVignette()'. To cite Bioconductor, see
>    'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: limma
> Loading required package: affy
>    
>> x<-readQpcr("RAT_CT2.csv")
>> slotNames(x)
>>      
> [1] "geneNames"  "plateIndex" "exprs"      "normalized" "normGenes"
>    
>> rm(x)
>>      
>
>
>    
>> x<-readQpcrBatch()
>>      
> Error in initialize(value, ...) :
>    no slot of name "primerNames" for this object of class "qpcrBatch"
>
>
>
>    
>> sessionInfo()
>>      
> R version 2.13.0 (2011-04-13)
> Platform: i386-redhat-linux-gnu (32-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8
>   [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8
>   [7] LC_PAPER=en_GB.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] qpcrNorm_1.8.0 affy_1.28.1    limma_3.6.9    Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.18.0         preprocessCore_1.12.0
>    
>> traceback()
>>      
> 4: initialize(value, ...)
> 3: initialize(value, ...)
> 2: new("qpcrBatch", geneNames = x at primerNames, plateIndex = x at plateIndex,
>         exprs = x.data, normalized = FALSE, normGenes = x at normGenes)
> 1: readQpcrBatch()
>
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