[BioC] .Rnw file

[Lana Schaffer]

Wolfgand,
> sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
 [1] "splines"   "grid"      "tools"     "methods"   "stats"     "graphics" 
"grDevices" "utils"
 [9] "datasets"  "base"

other attached packages:
 davidTiling           GO  tilingArray       pixmap  geneplotter 
annotate   genefilter     survival
     "1.0.4"     "1.14.1"     "1.12.0"      "0.4-5"     "1.12.0" 
"1.12.1"     "1.12.0"       "2.29"
         vsn  strucchange     sandwich          zoo RColorBrewer 
affy       affyio      Biobase
    "1.12.0"      "1.3-1"      "2.0-1"      "1.2-1"      "0.2-3" 
"1.12.2"      "1.2.0"     "1.12.2"
>
Thanks,
Lana
----- Original Message ----- 
From: "Wolfgang Huber" <huber at ebi.ac.uk>
To: "Lana Schaffer" <schaffer at scripps.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Wednesday, January 03, 2007 12:50 PM
Subject: Re: [BioC] .Rnw file


>
> 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]]
>>>>
>>>> _______________________________________________
>>>> 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
>
>
> -- 
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>