[BioC] .Rnw file

[Lana Schaffer]

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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>
>