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Question: One-Color Agilent Data into Limma GUI
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gravatar for elliot harrison
10.9 years ago by
elliot harrison230 wrote:
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 > > > This message has been scanned for viruses by > BlackSpider...{{dropped:3}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology Shared Resource Director Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (208) 667-2793 This message has been scanned for viruses by BlackSpider...{{dropped:3}}
ADD COMMENTlink modified 10.9 years ago by J.delasHeras@ed.ac.uk1.9k • written 10.9 years ago by elliot harrison230
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gravatar for J.delasHeras@ed.ac.uk
10.9 years ago by
United Kingdom
J.delasHeras@ed.ac.uk1.9k wrote:
Quoting elliot harrison <e.harrison at="" epistem.co.uk="">: > 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? It's not a bad idea, it just cannot be done :-) Normalisation within arrays aims to "balance" the two signals on a 2-colour array. If you only have one colour... then you only normalise between samples/arrays. Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
ADD COMMENTlink written 10.9 years ago by J.delasHeras@ed.ac.uk1.9k
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