Chr Info for array CGH - agilent 60K
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Cian Murphy ▴ 40
@cian-murphy-6091
Last seen 4.3 years ago
United Kingdom
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]]
CGH CGH • 1.1k views
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