[BioC] Problems with oligo package : Nimblegen microarray analysis

[Benilton Carvalho]

you have a typo in your code.

you passed 'chanel', where it expected 'channel'.

best

On 19 October 2010 08:44, Michael MOZAR <mozemaster at gmail.com> wrote:
>> 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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