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

[Lin, Michael W.]

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!

 


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