[BioC] read.marrayInfo error

[Paul Boutros]

Hi all,

I'm having some difficulties using the read.marrayInfo method of the
marrayInput package.

Basically, I get an unusual error message after a few seconds of
processing.

=======================================================
> rat.layout <- read.marrayLayout(fname = fname, ngr=4, ngc=12, nsr=25,
nsc=26, skip=53, ctl.col=4, pl.col=5);
> rat.layout;
Array layout:    Object of class marrayLayout. 

Total number of spots:                  31200
Dimensions of grid matrix:              4 rows by 12 cols
Dimensions of spot matrices:            25 rows by 26 cols

Currently working with a subset of 31200 spots.

Control spots: 
There are   9935 types of controls : 
   3x SSC      Arab     Mm.10 Mm.100049 Mm.100060  Mm.10009 Mm.100099
Mm.100113 Mm.100117 Mm.100131 
       98       480         2         2         2         2         2
2         2         2 
...

Notes on layout: 
c:/docume~1/paul/dev/input/GP_M15k1.gal
> rat.names <- read.marrayInfo(fname=fname, info.id=5, labels=5, skip=53);
Error in "maInfo<-"(*tmp*, value = dat[, info.id]) : 
        No direct or inherited method for function "maInfo<-" for this
call
> traceback();
2: "maInfo<-"(*tmp*, value = dat[, info.id])
1: read.marrayInfo(fname = fname, info.id = 5, labels = 5, skip = 53)
=======================================================


I'm not too clear what's going on here.  In case it helps, here is the
first bit of my GAL input file.

ATF	1.0
51	5
Type=GenePix ArrayList V1.0
BlockCount=48
BlockType=0
"Block1= 3000, 3000, 110, 26, 167, 25, 167" 
"Block2= 7500, 3000, 110, 26, 167, 25, 167" 
"Block3= 12000, 3000, 110, 26, 167, 25, 167" 
"Block4= 16500, 3000, 110, 26, 167, 25, 167" 
"Block5= 3000, 7500, 110, 26, 167, 25, 167" 
"Block6= 7500, 7500, 110, 26, 167, 25, 167" 
"Block7= 12000, 7500, 110, 26, 167, 25, 167" 
"Block8= 16500, 7500, 110, 26, 167, 25, 167" 
"Block9= 3000, 12000, 110, 26, 167, 25, 167" 
"Block10= 7500, 12000, 110, 26, 167, 25, 167" 
"Block11= 12000, 12000, 110, 26, 167, 25, 167" 
"Block12= 16500, 12000, 110, 26, 167, 25, 167" 
"Block13= 3000, 16500, 110, 26, 167, 25, 167" 
"Block14= 7500, 16500, 110, 26, 167, 25, 167" 
"Block15= 12000, 16500, 110, 26, 167, 25, 167" 
"Block16= 16500, 16500, 110, 26, 167, 25, 167" 
"Block17= 3000, 21000, 110, 26, 167, 25, 167" 
"Block18= 7500, 21000, 110, 26, 167, 25, 167" 
"Block19= 12000, 21000, 110, 26, 167, 25, 167" 
"Block20= 16500, 21000, 110, 26, 167, 25, 167" 
"Block21= 3000, 25500, 110, 26, 167, 25, 167" 
"Block22= 7500, 25500, 110, 26, 167, 25, 167" 
"Block23= 12000, 25500, 110, 26, 167, 25, 167" 
"Block24= 16500, 25500, 110, 26, 167, 25, 167" 
"Block25= 3000, 30000, 110, 26, 167, 25, 167" 
"Block26= 7500, 30000, 110, 26, 167, 25, 167" 
"Block27= 12000, 30000, 110, 26, 167, 25, 167" 
"Block28= 16500, 30000, 110, 26, 167, 25, 167" 
"Block29= 3000, 34500, 110, 26, 167, 25, 167" 
"Block30= 7500, 34500, 110, 26, 167, 25, 167" 
"Block31= 12000, 34500, 110, 26, 167, 25, 167" 
"Block32= 16500, 34500, 110, 26, 167, 25, 167" 
"Block33= 3000, 39000, 110, 26, 167, 25, 167" 
"Block34= 7500, 39000, 110, 26, 167, 25, 167" 
"Block35= 12000, 39000, 110, 26, 167, 25, 167" 
"Block36= 16500, 39000, 110, 26, 167, 25, 167" 
"Block37= 3000, 43500, 110, 26, 167, 25, 167" 
"Block38= 7500, 43500, 110, 26, 167, 25, 167" 
"Block39= 12000, 43500, 110, 26, 167, 25, 167" 
"Block40= 16500, 43500, 110, 26, 167, 25, 167" 
"Block41= 3000, 48000, 110, 26, 167, 25, 167" 
"Block42= 7500, 48000, 110, 26, 167, 25, 167" 
"Block43= 12000, 48000, 110, 26, 167, 25, 167" 
"Block44= 16500, 48000, 110, 26, 167, 25, 167" 
"Block45= 3000, 52500, 110, 26, 167, 25, 167" 
"Block46= 7500, 52500, 110, 26, 167, 25, 167" 
"Block47= 12000, 52500, 110, 26, 167, 25, 167" 
"Block48= 16500, 52500, 110, 26, 167, 25, 167" 
Block	Row	Column	Name	ID
1	1	1	Mm.142830	H3005F02
1	1	2	Mm.142830	H3005F02