[BioC] .Rnw file
Lana Schaffer
schaffer at scripps.edu
Wed Jan 3 21:10:10 CET 2007
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]]
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>
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>
>
> --
> ------------------------------------------------------------------
> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
>
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