[BioC] Normalize background on marray Agilent object

[Gordon K Smyth]

> Date: Mon, 15 Jul 2013 11:43:55 +0200
> From: Guillermo Marco Puche <guillermo.marco at sistemasgenomicos.com>
> To: bioconductor at r-project.org
> Subject: Re: [BioC] Normalize background on marray Agilent object
>
> Dear Gordon,
>
> That's the error message I'm getting while using your code:

You still don't seem to have tried the code I suggested.  I suggested 
read.maimages(), not read.Agilent().

Gordon

> Error in 1:n : NA/NaN argument
>
> I detail all the commands I'm previously using to try to find the problem.
>
> library(marray)
>
> input <- c("Arrays/UR0267/FE File/252206034056_SLOT01_S01_CytoCGH_0105_May11_1_1.txt")
>
> Sys.setlocale('LC_ALL','C')
>
> maData = read.Agilent(fnames=input , path=NULL, name.Gf
> ="gMedianSignal", name.Gb = "gBGMedianSignal", name.Rf ="rMedianSignal",
>  name.Rb = "rBGMedianSignal", name.W= NULL, layout =NULL, gnames = NULL,
>  targets = NULL, notes=NULL, skip=NULL, sep="\t", quote="\"",
> DEBUG=FALSE, info.id=NULL)
>
>
> Best regards,
> Guillermo.
>
> On 07/04/2013 01:39 AM, Gordon K Smyth wrote:
>> Dear Guillermo,
>>
>> I already gave you all the code you need to use.  The code already
>> parses the header for you.  Could you not posssibly try it before
>> asking more questions?
>>
>> Thanks
>> Gordon
>>
>>> Date: Wed, 03 Jul 2013 09:59:42 +0200
>>> From: Guillermo Marco Puche <guillermo.marco at sistemasgenomicos.com>
>>> To: bioconductor at r-project.org
>>> Cc: "James W. MacDonald" <jmacdon at uw.edu>
>>> Subject: Re: [BioC] Normalize background on marray Agilent object
>>>
>>> Hello,
>>>
>>> To read.maimages with Limma do you need to parse Agilent headers from
>>> txt files ? I had some troubles with marray pacakge using
>>> read.Agilent function.
>>>
>>> Best,
>>>
>>> Guillermo.
>>>
>>> On 06/21/2013 04:18 PM, James W. MacDonald wrote:
>>>> Hi Guillermo,
>>>>
>>>> On 6/21/2013 3:06 AM, Guillermo Marco Puche wrote:
>>>>> Dear Gordon,
>>>>>
>>>>> Thank you for your answer. I'll look further into Agilent array
>>>>> image files with limma.
>>>>>
>>>>> As I said the problem is that i'm not currently reading image from
>>>>> Agilent array, but the text data file with marray library and
>>>>> loading it into a maData object like this:
>>>>
>>>> Please note that the read.maimages function doesn't read image files
>>>> - it reads in the same text files you are reading with read.Agilent.
>>>>
>>>> Your original question had to do with the 'correct' background
>>>> correction to use for your Agilent array data. Gordon has therefore
>>>> suggested that you use the 'normexp' method in limma. This does of
>>>> course require you to switch to a different package, but limma tends
>>>> to get better support than marray, so you might be wise to make the
>>>> switch.
>>>>
>>>> But to your original point, you are asking a question that might not
>>>> have a definitive answer. There is no 'best' way to do a background
>>>> correction. There are methods that seem to do a reasonable job over
>>>> a range of experiments, and if I understand correctly, this is why
>>>> Gordon is suggesting you use normexp. But which method might be best
>>>> for your particular situation will be difficult for anybody to predict.
>>>>
>>>> Best,
>>>>
>>>> Jim
>>>>
>>>>
>>>>>
>>>>> maData = read.Agilent(fnames=input , path=NULL, name.Gf =
>>>>> "gMedianSignal", name.Gb = "gBGMedianSignal", name.Rf =
>>>>> "rMedianSignal", name.Rb = "rBGMedianSignal", name.W= NULL, layout =
>>>>> NULL, gnames = NULL, targets = NULL, notes=NULL, skip=NULL, sep="\t",
>>>>> quote="\"", DEBUG=FALSE, info.id=NULL)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On 06/20/2013 01:11 PM, Gordon K Smyth wrote:
>>>>>>> Dera Guillermo,
>>>>>>>
>>>>>>> The usual process is to (1) background correct the foreground
>>>>>>> intensities with respect to the background, then (2) normalize the
>>>>>>> M-values (log-ratios).
>>>>>>>
>>>>>>> For an Agilent two colour array, I do this by:
>>>>>>>
>>>>>>>    library(limma)
>>>>>>>    RG<- read.maimages(files, source="agilent")
>>>>>>>    RGb<- backgroundCorrect(RG, method="normexp")
>>>>>>>    MA<- normalizeWithinArrays(RGb, method="loess")
>>>>>>>
>>>>>>> although it is sometimes a good idea to remove positive control
>>>>>>> probes before the normalization step.
>>>>>>>
>>>>>>> A recent example using this pipeline is:
>>>>>>>
>>>>>>> http://www.biomedcentral.com/1471-2105/14/165
>>>>>>>
>>>>>>> Best wishes
>>>>>>> Gordon
>>>>>>>
>>>>>>>> Date: Wed, 19 Jun 2013 22:38:34 +0200
>>>>>>>> From: Guillermo Marco Puche<guillermo.marco at sistemasgenomicos.com>
>>>>>>>> To: "bioconductor at r-project.org"<bioconductor at r-project.org>
>>>>>>>> Subject: [BioC] Normalize background on marray Agilent object
>>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> I'm currently trying to normalize rBG values for a marray
>>>>>>>> object. Data origin is Agilent dual channel array. I've loaded
>>>>>>>> information with readAgilent() function.
>>>>>>>>
>>>>>>>> What's the correct way to normalize the data? I would like to
>>>>>>>> normalize background information first maNorm function manual
>>>>>>>> isn't very clarifying for me.
>>>>>>>>
>>>>>>>> Thanks !
>>>>>>>>
>>>>>>>> Best regards,
>>>>>>>> Guillermo.

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