[BioC] One-Color Agilent Data into Limma GUI

[elliot harrison]

Hi Martin,

Thanks for that.
On your advice I remade the targets file from scratch and what do you
know the data loaded.


So I went back to the original post I was using as a guide

1. Use read.maimages() with dummy arguments for R & Rb
Done
2. Background correct as usual using backgroundCorrect()
Done
3. Normalize the RG$G matrix using normalizeBetweenArrays()
Done
4. Use log2(RG$G) as input to lmFit() etc.
Done


They make no mention of normalising within arrays. Is this a bad idea
with one colour data?

Other than that I'm going great guns

Thanks Again

Elliott
 

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Tuesday, October 09, 2007 2:34 PM
To: elliot harrison
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] One-Color Aglent Data into Limma GUI

Hi Elliot,

"elliot harrison" <e.harrison at epistem.co.uk> writes:

> Hi All,
>  
> I'm trying to work with One-color agilent data without much luck.
> http://article.gmane.org/gmane.science.biology.informatics.conductor/1
> 28
> 18/match=agilent
>
> I've tried the above method but as I posted before I get stuck on the 
> following error.
>  
> Error in readGenericHeader(fullname, columns = columns, sep = sep) : 
> Specified column headings not found in file

Sorry your earlier post didn't get a reply. Try narrowing things down to
their essence, and post something as close to reproducible as possible.
I bet you end up with the problem here

targets <- ...
G <- read.maimages(targets,
                   columns = list(G = "gMeanSignal", Gb = "gBGUsed",
                     R = "gProcessedSignal", Rb = "gBGMedianSignal"))

The likely candidates are either that one of the 'targets' is incorrect,
or that one of the files pointed to by targets does not, or appears not,
to contain one of the columns. So the next challenge is to figure out
which file is problematic. I'd try 

> options(error=recover)

and then execute read.maimages. You'll then want to choose one of the
listed 'frames' (probably labeled something like readGenericHeader).
You'll be in something called the browser (see
?browser) and will be able to evaluate any R expression. In particular,
when you've navigated to the right frame (this might take a bit of
experimentation), you'll be able to print out 'fullname', the name of
the file you're having trouble with.

Your agilent files are likely text files, and you can likely look inside
them for strings matching the column names you've listed. If the column
names aren't found, then you've discovered why you're getting the error!
If they are found, then report back with a thoughtful and concise digest
of your discoveries. You do want to be careful not to 'save' files
you're looking at, unless you know your text editor won't try to be
'helpful' in some way, e.g., by saving the file in a different encoding.

Please also include the output of sessionInfo().

Martin

> As such I thought I'd try a different approach and have a go with the 
> LimmaGUI.
> I've faked green channel columns in my files like this which I hope to

> ignore once imported.
>
> FEATURES	FeatureNum	Block	Row	Col	SubTypeMask
> SubTypeName	ProbeUID	ControlType	ProbeName	GeneName
> 	SystematicName	PositionX	PositionY	gProcessedSignal
> rProcessedSignal	gMeanSignal	rMeanSignal
> 	gMedianSignal	rMedianSignal	gBGUsed	rBGUsed
> DATA	1	1	1	1	0		0	1
> GE_BrightCorner	GE_BrightCorner	GE_BrightCorner	9790.72	223.949
358.8079
> 1.52E+04	1.10E+04	1.10E+04	10446	10446	78.8743
> 78.8743
>
> When I try to import the files I gives an error saying it was unable 
> to read the image processing files
>
> I've also added a Block column as the next error is in getLayout(gal) 
> GAL file must contain Block, Column, Row error.
> Then Error in Matrix and other but I guess this is all due to the file

> not being read properly in the first place.
>
> I am using another analysis package as well so I am analysing my data 
> but there is so much more to R.
> Any help getting going would be greatly appreciated.
>
>
> Many Thanks
>
> Elliott
>
>
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--
Martin Morgan
Computational Biology Shared Resource Director Fred Hutchinson Cancer
Research Center 1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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