[prev in list] [next in list] [prev in thread] [next in thread] 

List:       bioconductor
Subject:    [BioC] Chr Info for array CGH - agilent 60K
From:       Cian Murphy <cian.murphy.11 () ucl ! ac ! uk>
Date:       2013-08-29 12:47:22
Message-ID: 521F42DA.7040307 () ucl ! ac ! uk
[Download RAW message or body]

Hello,

I have 60k Agilent array CGH data in the form of .txt and batch 
processed .cgh files. Neither appear readily import-able into R as there 
are no columns devoted entirely to Chr and Position. The .txt files have 
this info in columns interspersed with rows with things like 
"DarkCorner", or "HsCGHBrightCorner". Maybe this isn't the problem, but 
I get an error following the standard example:

Trying snapCGH:

 >    cgh_file <- read.maimages("file.txt", source="agilent")

 >    RG2 <- backgroundCorrect(cgh_file, method="minimum")

 >    MA <- normalizeWithinArrays(RG2, method="median")

 >    MA2 <- processCGH(MA,method.of.averaging=mean, ID = "ID")
         Error in processCGH(MA, method.of.averaging = mean, ID = "ID") :
         $design component is null

https://stat.ethz.ch/pipermail/bioconductor/2006-November/015003.html 
says this "$design component is null" error is because of a lack of Chr 
info. As I said it's clearly in the files, but how do I get R to see that?


The first row of the text files contains strings like "Type", "text", 
"integer", "float",

And advice?

Thanks,

Cian

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
[prev in list] [next in list] [prev in thread] [next in thread]