[BioC] using marrayInput package with GenePix .gpr file - read.GenePix()

Lin, Michael W. Lin.WoonTzuMichael at mayo.edu
Sat Nov 8 00:00:55 MET 2003



            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





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!


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