[BioC] HTqPCR error

[Heidi Dvinge]

Hi Deepak,

based on your description, I gather you're taking to the "Reference
Manual", and not the vignette which can also be opened directly from
within R using open.vignette()

The Reference Manual is generated automatically when the package is built.
It consist off all the example included in the package, i.e. all the pages
available via help() or "?". AFAIK there isn't any other pdf version
available, at least not one that's formatted differently. However, for
those examples you mention below, the same text can be accessed in R by
saying:

> ?'HTqPCR-package'
> ?clusterCt
> ?filterCategory

Incidentally, the lines expanding into the margins only list all available
arguments for each function, i.e. the same as listed under the "Arguments"
header.

HTH
\Heidi


> Hi Heidi,
>
> Thanks for your help with HTqPCR function earlier. I have one more
> inquiry.
>
> The reference manual i have downloaded from R website "HTqPCR.pdf", some
> text is merging into the margins so the commands are incomplete (eq, pages
> 2,5,7). Is there a new version or format of that document where I could
> have access to the hidden text.
>
> Your response will be much appreciated.
>
> Thanks,
> Deepak
>
>
> Classification:  UNCLASSIFIED
> Caveats: None
>
>
>>>> "Heidi Dvinge" <heidi at ebi.ac.uk> 2/9/2011 5:46 AM >>>
> Hi Deepak,
>
>> Hi there,
>>
>> I am encountering the an error while using "samples" argument in
>> "readCtData". I am basically trying to use sample names from a design
>> file
>> column rather than using file names.
>>
>>  raw <- readCtData(files=files$FileName, path=path, SDS=TRUE,
>> header=TRUE,
>> n.features=384, feature=4, type=5, position=1, Ct=6,
>> samples=files$SampleName)
>>
>> error is:
>>
>> Error in function (classes, fdef, mtable)  :
>>   unable to find an inherited method for function "sampleNames<-", for
>> signature "qPCRset", "factor"
>>
> unless you've read in your "files" object with something like
> read.delim(..., as.is=TRUE), then the content of each column is probably a
> factor rather than e.g. numeric or character. Does it work is you say?:
>
> raw <- readCtData(files=files$FileName, path=path, SDS=TRUE, header=TRUE,
> n.features=384, feature=4, type=5, position=1, Ct=6,
> samples=as.character(files$SampleName))
>
> HTH
> \Heidi
>
>>
>> Can you please comment how can i use this option.
>>
>> Thank you,
>> Deepak
>>
>> Classification:  UNCLASSIFIED
>> Caveats: None
>>
>>
>>
>> Classification:  UNCLASSIFIED
>> Caveats: None
>>
>>
>
>
>
>
> Classification:  UNCLASSIFIED
> Caveats: None
>
>