[BioC] .Rnw file

[Robert Gentleman]

Hi Lana,
   Using Rtangle("assessNorm.Rnw")
will give you a file named assessNorm.R with all the R code in it, that 
could be source'd if that is what you want to do

for now, as Steffen said, your code in chunk 8 is not working and you 
need to debug it, this has nothing to do with Sweave,

best wishes
   Robert

Steffen Durinck wrote:
> 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
>>>>
>>>
> 
> _______________________________________________
> 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
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org