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elliot harrison
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@elliot-harrison-2391
Last seen 9.6 years ago
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@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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Phone: (208) 667-2793
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