[BioC] using marrayInput package with GenePix .gpr file -
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:
> 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:
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.
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:
Thanks for your help!
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