[BioC] annotation

[Marcelo Brandão]

Hello.
Yes, it works!!!!
Thanks, now I am working on how to design my analysis.

Marcelo

Em 15 de agosto de 2010 19:08, Benilton Carvalho
<beniltoncarvalho at gmail.com> escreveu:
> 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
>>
>



-- 
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