[BioC] annotation

[Benilton Carvalho]

update

vmd <- data.frame(labelDescription = "Treatment applied to samples")

to

vmd <- data.frame(labelDescription = "Treatment applied to samples",
channel=factor("_ALL_", levels=c("exprs", "_ALL_"))

and let me know how it goes,
b

2010/8/15 Marcelo Brandão <brandao.marcelo at gmail.com>:
> Hi there
> Thanks for the script.
> But i think there is something broken or, probably, I am doing something wrong.
> Here is what I use:
>
>>source('http://bioconductor.org/biocLite.R')
> .
> .
> .
>>library(oligo)
> .
> .
> .
> ================================================================================
> Welcome to oligo version 1.12.2
> ================================================================================
>> xys <- list.xysfiles()
>> ddf <- data.frame(group = rep(c("experimental", "control", "mutated"),each=4), row.names=xys)
>> vmd <- data.frame(labelDescription = "Treatment applied to samples")
>> pdt <- new("AnnotatedDataFrame", data=ddf, varMetadata=vmd)
>> rawData <- read.xysfiles(xys, phenoData=pdt)
> Loading required package: pd.2006.08.18.ti4932.60mer
> Loading required package: RSQLite
> Loading required package: DBI
> Platform design info loaded.
> Checking designs for each XYS file... Done.
> Allocating memory... Done.
> Reading 50186202_532.xys.
> Reading 50194302_532.xys.
> Reading 50194402_532.xys.
> Reading 50196202_532.xys.
> Reading 50198502_532.xys.
> Reading 50201302_532.xys.
> Reading 50204102_532.xys.
> Reading 50204202_532.xys.
> Reading 50204302_532.xys.
> Reading 50207902_532.xys.
> Reading 50208002_532.xys.
> Reading 50208102_532.xys.
> Error in validObject(out) :
>  invalid class "ExpressionFeatureSet" object:
>  'NChannelSet' varMetadata must have a 'channel' column
>> rawData$group
> Error: object 'rawData' not found
>
> It seems that I need a channel column somewhere. And here is my question, Where?
>
> Well, thanks for any help
>
> My best wishes
>
> Marcelo
>
>
> Em 13 de agosto de 2010 13:44, Benilton Carvalho
> <beniltoncarvalho at gmail.com> escreveu:
>> you should create the appropriate phenoData object and pass it to
>> read.xysfiles (if you're using 'oligo').
>>
>> eg.:
>>
>> library(oligo)
>> xys <- list.xysfiles()
>> ddf <- data.frame(group = rep(c("experimental", "control", "mutated"),
>> each=4), row.names=xys)
>> vmd <- data.frame(labelDescription = "Treatment applied to samples")
>> pdt <- new("AnnotatedDataFrame", data=ddf, varMetadata=vmd)
>> rawData <- read.xysfiles(xys, phenoData=pdt)
>> rawData$group
>>
>> b
>>
>> 2010/8/13 Marcelo Brandão <brandao.marcelo at gmail.com>:
>>> Hello there
>>> I am using Bioc to analyze a Nimblegen Microarray. Everything seems to
>>> be smoothly working. I would like to ask for some help, I have 12 xys
>>> files, and wander if there is a way to "annotate" each one of them as
>>> experimental, control or mutated. So, when I will perform any
>>> comparison there is any way to design the experiment as designEsp <-
>>> cbind(Grp1=1,Grp2vs1=c(control,mutated)) ?
>>>
>>> Complicated? Well, to simplify:
>>> there is a way to simply say to Bioc: "now I will analyze control
>>> versus experimental."
>>>
>>> Many thanks in advance.
>>>
>>> Marcelo
>>>
>>> --
>>> Marcelo Mendes Brandão
>>> Postdoc fellow
>>> Laboratório de Biologia Molecular de Plantas - ESALQ/USP
>>> Website: http://bioinfo.esalq.usp.br
>>> AtPIN: http://bioinfo.esalq.usp.br/atpin
>>> SKYPE: mmbrand
>>> Tel: (+55) 19 3429 4442
>>>
>>> _______________________________________________
>>> 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
>>>
>>
>
>
>
> --
> Marcelo Mendes Brandão
> Postdoc fellow
> Laboratório de Biologia Molecular de Plantas - ESALQ/USP
> Website: http://bioinfo.esalq.usp.br
> AtPIN: http://bioinfo.esalq.usp.br/atpin
> SKYPE: mmbrand
> Tel: (+55) 19 3429 4442
>