using marrayInput package with GenePix .gpr file - read.GenePix()
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@lin-michael-w-523
Last seen 8.6 years ago
Hi: We are learning to use the marray suites of packages for our spotted array data analysis. I have encountered problem that I can not resolve. I wonder if someone can help me identify what I am doing wrong here. In this case I am creating a marrayRaw object from a .gpr file that only contains one array. My code looks like the following: > library(marrayInput) > rawdata <- read.GenePix("test00.gpr") This created a marraRaw object "rawdata" for me, but when I go on to examine it, it appeared to have no data. The following information (in blue text) is given when I type "rawdata" at te command prompt: > rawdata Pre-normalization intensity data: Object of class marrayRaw. Number of arrays: 1 arrays. A) Layout of spots on the array: Array layout: Object of class marrayLayout. Total number of spots: Dimensions of grid matrix: rows by cols Dimensions of spot matrices: rows by cols Currently working with a subset of spots. Control spots: Notes on layout: B) Samples hybridized to the array: Object of class marrayInfo. NULL data frame with 1 rows Number of labels: 0 Dimensions of maInfo matrix: 0 rows by 0 columns Notes: C) Summary statistics for log-ratio distribution: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's test00.gpr -3.52 -0.24 -0.02 0.02 0.11 4.62 11 D) Notes on intensity data: GenePix Data Thanks for your help! [[alternative HTML version deleted]]
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@jean-yee-hwa-yang-104
Last seen 8.6 years ago
Hi Michael, The data is there, there is no information about the layout at the moment. The log-ratios can be obtained using maM(rawdata). To read in layout information, you can do it two ways: A) info <- read.Galfile("test00.gpr") maLayout(rawdata) <- info$layout maGnames(rawdata) <- info$gnames B) rawdata <- gpTools("test00.gpr", galfile="test00.gpr", raw=TRUE, plot=FALSE, quality=FALSE) Either way, you will need to use maM(rawdata) to look at the log- ratios and maA(rawdata) to obtain the log-intensity information. Cheers Jean > This created a marraRaw object "rawdata" for me, but when > I go on to examine it, it appeared to have no data. The following > information (in blue text) is given when I type "rawdata" at te > command prompt: > > > > > rawdata > > Pre-normalization intensity data: Object of class marrayRaw. > > > > Number of arrays: 1 arrays. > > > > A) Layout of spots on the array: > > Array layout: Object of class marrayLayout. > > > > Total number of spots: > > Dimensions of grid matrix: rows by cols > > Dimensions of spot matrices: rows by cols > > > > Currently working with a subset of spots. > > > > Control spots: > > > > > > Notes on layout: > > > > > > B) Samples hybridized to the array: > > Object of class marrayInfo. > > > > NULL data frame with 1 rows > > > > Number of labels: 0 > > Dimensions of maInfo matrix: 0 rows by 0 columns > > > > Notes: > > > > > > C) Summary statistics for log-ratio distribution: > > Min. 1st Qu. Median Mean 3rd Qu. Max. NA's > > test00.gpr -3.52 -0.24 -0.02 0.02 0.11 4.62 11 > > > > D) Notes on intensity data: > > GenePix Data > > > > > > Thanks for your help! > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >