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

[Jean Yee Hwa Yang]

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 at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>