[BioC] annotation

[Marcelo Brandão]

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