> hi
> i try to make an analysis of a micro array from nimblegen (oligonucleotides
> one channel) for example to do a boxplot
> i follow the instruction in the pdf "02 - NimbleGen Expression and
> Preprocessing"
> but i don't know how to make this,  with one channel, how can i do ?
>
> here my code :
>
> > xys.files <-list.xysfiles(full.names = TRUE)
> > xys.files
> [1] "./88693_532.xys" "./89430_532.xys" "./96225_532.xys" "./96252_532.xys"
> > basename(xys.files)
> [1] "88693_532.xys" "89430_532.xys" "96225_532.xys" "96252_532.xys"
> > theData <-data.frame(Key = rep(c("cals", "embryon"), each = 2))
> > is.data.frame(theData)
> [1] TRUE
> > rownames(theData) <- basename(xys.files)
> > vm <- data.frame(chanel = factor("_ALL_", levels = c("channel1",
> "channel2", "_ALL_")), labelDescription = "oryza sativa")
> > pd <- new("AnnotatedDataFrame", data = theData, varMetadata = vm)
> > test <-read.xysfiles(xys.files, phenoData = pd)
>
> when i do this i got the error :
>
> > test <-read.xysfiles(xys.files, phenoData = pd)
> Platform design info loaded.
> Checking designs for each XYS file... Done.
> Allocating memory... Done.
> Reading ./88693_532.xys.
> Reading ./89430_532.xys.
> Reading ./96225_532.xys.
> Reading ./96252_532.xys.
> Erreur dans validObject(out) :
>   invalid class "ExpressionFeatureSet" object:
>   'NChannelSet' varMetadata must have a 'channel' column
>
>
> here my session info () :
>
> R version 2.11.1 (2010-05-31)
> x86_64-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=fr_FR.utf8       LC_NUMERIC=C
>  [3] LC_TIME=fr_FR.utf8        LC_COLLATE=fr_FR.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=fr_FR.utf8
>  [7] LC_PAPER=fr_FR.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] pd.2006.07.24.picaud.dbretro_0.0.1 RSQLite_0.9-2
>  [3] DBI_0.2-5                          RColorBrewer_1.0-2
>  [5] limma_3.4.5                        genefilter_1.30.0
>  [7] maqcExpression4plex_1.2            oligo_1.12.2
>  [9] oligoClasses_1.10.0                Biobase_2.8.0
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.20.0     affyio_1.16.0         annotate_1.26.1
>  [4] AnnotationDbi_1.10.2  Biostrings_2.16.9     IRanges_1.6.17
>  [7] preprocessCore_1.10.0 splines_2.11.1        survival_2.35-8
> [10] tools_2.11.1          xtable_1.5-6
>
> and my traceback ()
>
> > traceback()
> 3: stop(msg, " ", errors, domain = NA)
> 2: validObject(out)
> 1: read.xysfiles(xys.files, phenoData = pd)
> --
> MOZAR Michaël
> Master Bioinformatique
> Université de Nantes
> 0688715937
>



-- 
MOZAR Michaël
Master Bioinformatique
Université de Nantes
0688715937

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