[BioC] .Rnw file

[Wolfgang Huber]

Dear Lana,

Can you please try with tilingArray from the development branch
http://www.bioconductor.org/packages/2.0/bioc/html/tilingArray.html
and see if you can reproduce this?

I have no idea what could cause your problem reported below, and have 
not seen it before (however I have never used the Windows-version of R 
for this).

Has anyone else seen this error for these data?

   Best wishes
     Wolfgang



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


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