[BioC] .Rnw file

[Steffen Durinck]

It looks like you were building the vignette but the code got stuck 
while executing code chunk 8.
Try to find out why this part of the code didn't work, change the code 
and run Sweave again.
You could first try to run the code manually by copy-pasting the code 
chunks in your R console and make sure they work before running Sweave.

best,
Steffen

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]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: 
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>>