[BioC] .Rnw file

[Wolfgang Huber]

Dear Lana,
what is the output of "sessionInfo()"?
  Best wishes
   Wolfgang


Lana Schaffer wrote:
> Steffen,
>> Sweave("assessNorm.Rnw")
>> Sweave("assessNorm.Rnw")
> Writing to file assessNorm.tex
> Processing code chunks ...
>  1 : echo term hide (label=load)
>  2 : term verbatim (label=errorReporting)
>  3 : echo term verbatim (label=showDavidTilingData)
>  4 : echo term verbatim (label=probeAnno)
>  5 : echo term verbatim (label=whPM)
>  6 : echo term verbatim (label=table)
>  7 : echo term verbatim (label=selectArrays)
>  8 : echo term verbatim (label=normalizeByReference)
> 
> Error:  chunk 8 (label=normalizeByReference)
> Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose = verbose) 
> :
> 
> The likelihood optimization did not converge. A likely reason is that the 
> normalization parameters are not uniquely identifiable from the provided 
> data.
> Possibly, the columns of the data matrix are exactly co-linear or affine 
> dependent - please verify the data to make sure there were no mix-ups.
> 
> Enter a frame number, or 0 to exit
> 
> 1: Sweave("assessNorm.Rnw")
> 2: driver$runcode(drobj, chunk, chunkopts)
> 3: RweaveTryStop(err, options)
> 
> ----- Original Message ----- 
> From: "Steffen Durinck" <durincks at mail.nih.gov>
> To: "Lana Schaffer" <schaffer at scripps.edu>
> Cc: <bioconductor at stat.math.ethz.ch>
> Sent: Wednesday, January 03, 2007 10:55 AM
> Subject: Re: [BioC] .Rnw file
> 
> 
>> Hi Lana,
>>
>> Try:
>>
>> Sweave("assessNorm.Rnw")
>>
>> best,
>> Steffen
>>
>> Lana Schaffer wrote:
>>> Hi,
>>> I am a little confused how to use the .Rnw file to make a vignette.
>>> Instructions say "source file inst/scripts/assessNorm.Rnw"
>>> but when I use the command :  source("assessNorm.Rnw")
>>> I get an error:
>>> Error in parse(file, n = -1, NULL, "?") : syntax error at
>>> 1: %\VignetteIndexEntry{tilingArray - assess normalization}
>>>
>>> probably because it is not an R file.
>>> Would you straighten me out a bit?
>>>
>>> Lana Schaffer
>>> Biostatistics/Informatics
>>> The Scripps Research Institute
>>> DNA Array Core Facility
>>> La Jolla, CA 92037
>>> (858) 784-2263
>>> (858) 784-2994
>>> schaffer at scripps.edu
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
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>>
> 
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-- 
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber