[BioC] Problem about extracting interest data from NimbleGen oligo array

[Benilton Carvalho]

Maggie,

seriously, **please keep this on the mailing list**.

For the moment, keep your code simple:

library(oligo)
raw <- read.xysfiles(xys.files)
eset <- rma(raw)

Then inspect the featureNames(eset).

best,
b

2011/7/20 陈娟 <gtzxchj at hotmail.com>:
> Dear Professor,
> Thank you for your reply!
> In my opinion, the genomic annotation you meant is the annotation package I
> made beforehand("pd.090319.zea.kr.exptil"), yeah? I  have written part of my
> script and the error I run into below so that you can exam it and help me
> with it!
>
>>library("pd.090319.zea.kr.exptil")
>
>> maqc <- read.xysfiles(xys.files)
>
>> pd <- list.files(dir ,pattern = "phenoData",full.names = TRUE)
>
>> phenoData(maqc) <- read.AnnotatedDataFrame(pd)
>
>> class(maqc)
>
>> eset <- rma(maqc)
>
> Background correcting
>
> Normalizing
>
> Calculating Expression
>
> error in : validObject(out) :
>
>   invalid class "ExpressionSet" object: 1: sampleNames differ between
> assayData and phenoData
>
> invalid class "ExpressionSet" object: 2: sampleNames differ between
> phenoData and  protocolData
>
> Thank you very much!!
>
> Best Regards
>
> Maggie
>
>> From: beniltoncarvalho at gmail.com
>> Date: Wed, 20 Jul 2011 12:11:34 +0100
>> Subject: Re: [BioC] Problem about extracting interest data from NimbleGen
>> oligo array
>> To: gtzxchj at hotmail.com
>>
>> Maggie,
>>
>> You need to provide more details and exactly what you have done so
>> far. From what you describe, after preprocessing your data, you need
>> to load the you refer to and merge with the
>> preprocessed results.
>>
>> Please, keep this conversation on the mailing list, so others can benefit.
>>
>> b
>>
>> On 20 July 2011 02:03, 陈娟 <gtzxchj at hotmail.com> wrote:
>> >
>> > Dear Professor,I have searched many relevant questions about my topic in
>> > mailing list, but why can't I read them from my computer. It always warns:
>> > unable to visit, so I have to submit my problem via email. I learned from
>> > databases that the ID of Nimblegen probes are members of gene ID. I use
>> > commands such as agrep("GRMZM2G425430_T01",featureNames(eset))  to extract
>> > the location info of the data I need, but it always returned
>> > :integer(0).Could you tell me why and  How can I find the data of interest
>> > correctly from NimbleGen expression array?Thanks a lot!!Yours
>> > sincerelyMaggie
>> >        [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > Search the archives:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>>
>>
>>
>> --
>> Successful people ask better questions, and as a result, they get
>> better answers. (Tony Robbins)
>



-- 
Successful people ask better questions, and as a result, they get
better answers. (Tony Robbins)