btw, chapter 5 on this old document might be of interest.

http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/vignettes/oligo/inst/doc/primer.pdf


2014-02-21 8:19 GMT-03:00 Benilton Carvalho <beniltoncarvalho@gmail.com>:

> Hi James,
>
> please allow me to fix the code I gave you initially.
>
> pms = pm(rawTilingData)
> nc = ncol(pms)
> pns = probeNames(rawTilingData)
> res = basicRMA(cbind(pms[,,1], pms[,,2]), pns)
> res2 = new('NChannelSet', channel1=res[,1:nc], channel2=res[, -c(1:nc)])
>
> the reason I'm suggesting the use of an NChannelSet is because
> conceptually a 'TilingFeatureSet' is a container for raw data.
>
> benilton
>
>
>
> 2014-02-20 17:46 GMT-03:00 James Yousin <yousin.james@gmail.com>:
>
>
>> Thank you a lot for your help. This works.
>> I am trying to perform the ACME after this
>>
>> info <- getNgsColorsInfo(baseDirData, full = TRUE)
>> rawTilingData <- read.xysfiles2(info[,2], info[,1], sampleNames=info[,3])
>>
>> pms = pm(rawTilingData)
>> pns = probeNames(rawTilingData)
>> res = basicRMA(pms, pns)
>>
>> res2 <- new("TilingFeatureSet", exprs=res)
>>
>> // I think here I am having trouble creating an TilingArray Feature set
>> object, is it possible to create a TilingFeatureSet object after I have
>> performed normalization ?
>>
>> c1 <- channel(res2, "channel1")
>> c2 <- channel(res2, "channel2")
>>
>>
>> On Wed, Feb 19, 2014 at 7:05 PM, Benilton Carvalho <
>> beniltoncarvalho@gmail.com> wrote:
>>
>>> For tiling arrays, one often prefers to apply a different strategy for
>>> preprocessing.
>>>
>>> But if it's something you really want to do, you can extract the pms and
>>> do it "manually":
>>>
>>> pms = pm(xys)
>>> pns = probeNames(xys)
>>> res = basicRMA(pms, pns)
>>>
>>> b
>>>
>>>
>>> 2014-02-19 20:25 GMT-03:00 James Yousin <yousin.james@gmail.com>:
>>>
>>>> I am trying to do preprocessing on xys files and have used the
>>>> pdInfoBuilder package to successfully build the annotation files,
>>>> everything works until rma(), if I skip it I also get the results using
>>>> ACME. But I would like to know why rma() didnt work with xys files.
>>>>
>>>>
>>>> class(xys)
>>>> [1] "TilingFeatureSet"
>>>> attr(,"package")
>>>> [1] "oligoClasses"
>>>>
>>>> rma(xys)
>>>> Error in (function (classes, fdef, mtable) :
>>>> unable to find an inherited method for function 'rma' for signature
>>>> '"TilingFeatureSet"'
>>>>
>>>> is this happening because the object is not of any of the
>>>> "ExonFeatureSet",
>>>> "ExpressionFeatureSet", "GeneFeatureSet" or "SnpCnvFeatureSet".
>>>>
>>>> I do see elsewhere people got it to work on XYS files
>>>>
>>>> https://stat.ethz.ch/pipermail/bioconductor/2013-June/053378.html
>>>>
>>>> Thanks
>>>>
>>>> James
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
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>>>
>>>
>>
>

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