[BioC] limma layout query (genepix GAL file)

Fri Sep 30 11:50:58 CEST 2005

Hi
using R version 2.1.1
limma version 1.9.6

We know our Slide layout is
$ngrid.r
[1] 12
$ngrid.c
[1] 2
$nspot.r
[1] 7
$nspot.c
[1] 32
$ndups
[1] 2
$spacing
[1] 224
$npins
[1] 12
$start
[1] "topleft"
however when we read in layout from GAL file as below
RG$genes<-readGAL("M64_AtSSH_correct.gal")
RG$genes$Status<-controlStatus(spottypes, RG)
RG$printer<-getLayout(RG$genes)

we get

$ngrid.r
[1] 6
$ngrid.c
[1] 4
$nspot.r
[1] 7
$nspot.c
[1] 32

can you explain why this does not correspond to our expected layout?
below  is an extract of first 2 blocks from our GAL file
"M64_AtSSH_correct.gal" from Genepix version 5.1
The remaining 22 block follow the same row and column patterns.

thanks
Dave Berger

ATF 1
28 5
Type=GenePix ArrayList V1.0
BlockCount=24
BlockType=0
URL=http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=[ID]
Block1=2067, 2537, 200, 32, 280, 7, 281
Block2=11490, 2510, 200, 32, 280, 7, 281
Block3=2070, 7020, 200, 32, 280, 7, 281
Block4=11500, 7010, 200, 32, 280, 7, 281
Block5=2100, 11510, 200, 32, 280, 7, 281
Block6=11520, 11480, 200, 32, 280, 7, 281
Block7=2110, 15980, 200, 32, 280, 7, 281
Block8=11530, 15980, 200, 32, 280, 7, 281
Block9=2100, 20450, 200, 32, 280, 7, 281
Block10=11530, 20430, 200, 32, 280, 7, 281
Block11=2140, 24930, 200, 32, 280, 7, 281
Block12=11560, 24890, 200, 32, 280, 7, 281
Block13=2160, 29470, 200, 32, 280, 7, 281
Block14=11580, 29460, 200, 32, 280, 7, 281
Block15=2160, 33860, 200, 32, 280, 7, 281
Block16=11590, 33840, 200, 32, 280, 7, 281
Block17=2190, 38450, 200, 32, 280, 7, 281
Block18=11610, 38440, 200, 32, 280, 7, 281
Block19=2240, 42820, 200, 32, 280, 7, 281
Block20=11670, 42800, 200, 32, 280, 7, 281
Block21=2230, 47400, 200, 32, 280, 7, 281
Block22=11650, 47380, 200, 32, 280, 7, 281
Block23=2250, 51850, 200, 32, 280, 7, 281
Block24=11680, 51830, 200, 32, 280, 7, 281
Block Row Column Name ID
1 1 1 cDNA AF1-A1
1 1 2 cDNA AF3-A1
1 1 3 cDNA AF1-B1
1 1 4 cDNA AF3-B1
1 1 5 cDNA AF1-C1
1 1 6 cDNA AF3-C1
1 1 7 cDNA AF1-D1
1 1 8 cDNA AF3-D1
1 1 9 cDNA AF1-E1
1 1 10 cDNA AF3-E1
1 1 11 cDNA AF1-F1
1 1 12 cDNA AF3-F1
1 1 13 cDNA AF1-G1
1 1 14 cDNA AF3-G1
1 1 15 cDNA AF1-H1
1 1 16 cDNA AF3-H1
1 1 17 cDNA AF1-A7
1 1 18 cDNA AF3-A7
1 1 19 cDNA AF1-B7
1 1 20 cDNA AF3-B7
1 1 21 cDNA AF1-C7
1 1 22 cDNA AF3-C7
1 1 23 cDNA AF1-D7
1 1 24 cDNA AF3-D7
1 1 25 cDNA AF1-E7
1 1 26 cDNA AF3-E7
1 1 27 cDNA AF1-F7
1 1 28 cDNA AF3-F7
1 1 29 cDNA AF1-G7
1 1 30 cDNA AF3-G7
1 1 31 cDNA AF1-H7
1 1 32 cDNA AF3-H7
1 2 1 cDNA AF5-A1
1 2 2 cDNA SF1-A1
1 2 3 cDNA AF5-B1
1 2 4 cDNA SF1-B1
1 2 5 cDNA AF5-C1
1 2 6 cDNA SF1-C1
1 2 7 cDNA AF5-D1
1 2 8 cDNA SF1-D1
1 2 9 cDNA AF5-E1
1 2 10 cDNA SF1-E1
1 2 11 cDNA AF5-F1
1 2 12 cDNA SF1-F1
1 2 13 cDNA AF5-G1
1 2 14 cDNA SF1-G1
1 2 15 cDNA AF5-H1
1 2 16 cDNA SF1-H1
1 2 17 cDNA AF5-A7
1 2 18 cDNA SF1-A7
1 2 19 cDNA AF5-B7
1 2 20 cDNA SF1-B7
1 2 21 cDNA AF5-C7
1 2 22 cDNA SF1-C7
1 2 23 cDNA AF5-D7
1 2 24 cDNA SF1-D7
1 2 25 cDNA AF5-E7
1 2 26 cDNA SF1-E7
1 2 27 cDNA AF5-F7
1 2 28 cDNA SF1-F7
1 2 29 cDNA AF5-G7
1 2 30 cDNA SF1-G7
1 2 31 cDNA AF5-H7
1 2 32 cDNA SF1-H7
1 3 1 cDNA SF3-A1
1 3 2 cDNA SF5-A1
1 3 3 cDNA SF3-B1
1 3 4 cDNA SF5-B1
1 3 5 cDNA SF3-C1
1 3 6 cDNA SF5-C1
1 3 7 cDNA SF3-D1
1 3 8 cDNA SF5-D1
1 3 9 cDNA SF3-E1
1 3 10 cDNA SF5-E1
1 3 11 cDNA SF3-F1
1 3 12 cDNA SF5-F1
1 3 13 cDNA SF3-G1
1 3 14 cDNA SF5-G1
1 3 15 cDNA SF3-H1
1 3 16 cDNA SF5-H1
1 3 17 cDNA SF3-A7
1 3 18 cDNA SF5-A7
1 3 19 cDNA SF3-B7
1 3 20 cDNA SF5-B7
1 3 21 cDNA SF3-C7
1 3 22 cDNA SF5-C7
1 3 23 cDNA SF3-D7
1 3 24 cDNA SF5-D7
1 3 25 cDNA SF3-E7
1 3 26 cDNA SF5-E7
1 3 27 cDNA SF3-F7
1 3 28 cDNA SF5-F7
1 3 29 cDNA SF3-G7
1 3 30 cDNA SF5-G7
1 3 31 cDNA SF3-H7
1 3 32 cDNA SF5-H7
1 4 1 cDNA AR1-A1
1 4 2 cDNA AR3-A1
1 4 3 cDNA AR1-B1
1 4 4 cDNA AR3-B1
1 4 5 cDNA AR1-C1
1 4 6 cDNA AR3-C1
1 4 7 cDNA AR1-D1
1 4 8 cDNA AR3-D1
1 4 9 cDNA AR1-E1
1 4 10 cDNA AR3-E1
1 4 11 cDNA AR1-F1
1 4 12 cDNA AR3-F1
1 4 13 cDNA AR1-G1
1 4 14 cDNA AR3-G1
1 4 15 cDNA AR1-H1
1 4 16 cDNA AR3-H1
1 4 17 cDNA AR1-A7
1 4 18 cDNA AR3-A7
1 4 19 cDNA AR1-B7
1 4 20 cDNA AR3-B7
1 4 21 cDNA AR1-C7
1 4 22 cDNA AR3-C7
1 4 23 cDNA AR1-D7
1 4 24 cDNA AR3-D7
1 4 25 cDNA AR1-E7
1 4 26 cDNA AR3-E7
1 4 27 cDNA AR1-F7
1 4 28 cDNA AR3-F7
1 4 29 cDNA AR1-G7
1 4 30 cDNA AR3-G7
1 4 31 cDNA AR1-H7
1 4 32 cDNA AR3-H7
1 5 1 cDNA AR5-A1
1 5 2 cDNA SR1-A1
1 5 3 cDNA AR5-B1
1 5 4 cDNA SR1-B1
1 5 5 cDNA AR5-C1
1 5 6 cDNA SR1-C1
1 5 7 cDNA AR5-D1
1 5 8 cDNA SR1-D1
1 5 9 cDNA AR5-E1
1 5 10 cDNA SR1-E1
1 5 11 cDNA AR5-F1
1 5 12 cDNA SR1-F1
1 5 13 cDNA AR5-G1
1 5 14 cDNA SR1-G1
1 5 15 cDNA AR5-H1
1 5 16 cDNA SR1-H1
1 5 17 cDNA AR5-A7
1 5 18 cDNA SR1-A7
1 5 19 cDNA AR5-B7
1 5 20 cDNA SR1-B7
1 5 21 cDNA AR5-C7
1 5 22 cDNA SR1-C7
1 5 23 cDNA AR5-D7
1 5 24 cDNA SR1-D7
1 5 25 cDNA AR5-E7
1 5 26 cDNA SR1-E7
1 5 27 cDNA AR5-F7
1 5 28 cDNA SR1-F7
1 5 29 cDNA AR5-G7
1 5 30 cDNA SR1-G7
1 5 31 cDNA AR5-H7
1 5 32 cDNA SR1-H7
1 6 1 cDNA SR3-A1
1 6 2 cDNA SR5-A1
1 6 3 cDNA SR3-B1
1 6 4 cDNA SR5-B1
1 6 5 cDNA SR3-C1
1 6 6 cDNA SR5-C1
1 6 7 cDNA SR3-D1
1 6 8 cDNA SR5-D1
1 6 9 cDNA SR3-E1
1 6 10 cDNA SR5-E1
1 6 11 cDNA SR3-F1
1 6 12 cDNA SR5-F1
1 6 13 cDNA SR3-G1
1 6 14 cDNA SR5-G1
1 6 15 cDNA SR3-H1
1 6 16 cDNA SR5-H1
1 6 17 cDNA SR3-A7
1 6 18 cDNA SR5-A7
1 6 19 cDNA SR3-B7
1 6 20 cDNA SR5-B7
1 6 21 cDNA SR3-C7
1 6 22 cDNA SR5-C7
1 6 23 cDNA SR3-D7
1 6 24 cDNA SR5-D7
1 6 25 cDNA SR3-E7
1 6 26 cDNA SR5-E7
1 6 27 cDNA SR3-F7
1 6 28 cDNA SR5-F7
1 6 29 cDNA SR3-G7
1 6 30 cDNA SR5-G7
1 6 31 cDNA SR3-H7
1 6 32 cDNA SR5-H7
1 7 1 control CON_Bt
1 7 2 blank BLANK
1 7 3 control CON_GFP
1 7 4 blank BLANK
1 7 5 control CON_Globin
1 7 6 blank BLANK
1 7 7 control CON_GUS
1 7 8 blank BLANK
1 7 9 control CON_HPH
1 7 10 blank BLANK
1 7 11 control CON_Luc
1 7 12 blank BLANK
1 7 13 control CON_Bar
1 7 14 blank BLANK
1 7 15 control CON_nptII
1 7 16 blank BLANK
1 7 17 control CON_Sp1
1 7 18 blank BLANK
1 7 19 control CON_Sp2
1 7 20 blank BLANK
1 7 21 blank BLANK
1 7 22 blank BLANK
1 7 23 blank BLANK
1 7 24 blank BLANK
1 7 25 blank BLANK
1 7 26 blank BLANK
1 7 27 blank BLANK
1 7 28 blank BLANK
1 7 29 blank BLANK
1 7 30 blank BLANK
1 7 31 blank BLANK
1 7 32 blank BLANK
2 1 1 cDNA AF1-A1
2 1 2 cDNA AF3-A1
2 1 3 cDNA AF1-B1
2 1 4 cDNA AF3-B1
2 1 5 cDNA AF1-C1
2 1 6 cDNA AF3-C1
2 1 7 cDNA AF1-D1
2 1 8 cDNA AF3-D1
2 1 9 cDNA AF1-E1
2 1 10 cDNA AF3-E1
2 1 11 cDNA AF1-F1
2 1 12 cDNA AF3-F1
2 1 13 cDNA AF1-G1
2 1 14 cDNA AF3-G1
2 1 15 cDNA AF1-H1
2 1 16 cDNA AF3-H1
2 1 17 cDNA AF1-A7
2 1 18 cDNA AF3-A7
2 1 19 cDNA AF1-B7
2 1 20 cDNA AF3-B7
2 1 21 cDNA AF1-C7
2 1 22 cDNA AF3-C7
2 1 23 cDNA AF1-D7
2 1 24 cDNA AF3-D7
2 1 25 cDNA AF1-E7
2 1 26 cDNA AF3-E7
2 1 27 cDNA AF1-F7
2 1 28 cDNA AF3-F7
2 1 29 cDNA AF1-G7
2 1 30 cDNA AF3-G7
2 1 31 cDNA AF1-H7
2 1 32 cDNA AF3-H7
2 2 1 cDNA AF5-A1
2 2 2 cDNA SF1-A1
2 2 3 cDNA AF5-B1
2 2 4 cDNA SF1-B1
2 2 5 cDNA AF5-C1
2 2 6 cDNA SF1-C1
2 2 7 cDNA AF5-D1
2 2 8 cDNA SF1-D1
2 2 9 cDNA AF5-E1
2 2 10 cDNA SF1-E1
2 2 11 cDNA AF5-F1
2 2 12 cDNA SF1-F1
2 2 13 cDNA AF5-G1
2 2 14 cDNA SF1-G1
2 2 15 cDNA AF5-H1
2 2 16 cDNA SF1-H1
2 2 17 cDNA AF5-A7
2 2 18 cDNA SF1-A7
2 2 19 cDNA AF5-B7
2 2 20 cDNA SF1-B7
2 2 21 cDNA AF5-C7
2 2 22 cDNA SF1-C7
2 2 23 cDNA AF5-D7
2 2 24 cDNA SF1-D7
2 2 25 cDNA AF5-E7
2 2 26 cDNA SF1-E7
2 2 27 cDNA AF5-F7
2 2 28 cDNA SF1-F7
2 2 29 cDNA AF5-G7
2 2 30 cDNA SF1-G7
2 2 31 cDNA AF5-H7
2 2 32 cDNA SF1-H7
2 3 1 cDNA SF3-A1
2 3 2 cDNA SF5-A1
2 3 3 cDNA SF3-B1
2 3 4 cDNA SF5-B1
2 3 5 cDNA SF3-C1
2 3 6 cDNA SF5-C1
2 3 7 cDNA SF3-D1
2 3 8 cDNA SF5-D1
2 3 9 cDNA SF3-E1
2 3 10 cDNA SF5-E1
2 3 11 cDNA SF3-F1
2 3 12 cDNA SF5-F1
2 3 13 cDNA SF3-G1
2 3 14 cDNA SF5-G1
2 3 15 cDNA SF3-H1
2 3 16 cDNA SF5-H1
2 3 17 cDNA SF3-A7
2 3 18 cDNA SF5-A7
2 3 19 cDNA SF3-B7
2 3 20 cDNA SF5-B7
2 3 21 cDNA SF3-C7
2 3 22 cDNA SF5-C7
2 3 23 cDNA SF3-D7
2 3 24 cDNA SF5-D7
2 3 25 cDNA SF3-E7
2 3 26 cDNA SF5-E7
2 3 27 cDNA SF3-F7
2 3 28 cDNA SF5-F7
2 3 29 cDNA SF3-G7
2 3 30 cDNA SF5-G7
2 3 31 cDNA SF3-H7
2 3 32 cDNA SF5-H7
2 4 1 cDNA AR1-A1
2 4 2 cDNA AR3-A1
2 4 3 cDNA AR1-B1
2 4 4 cDNA AR3-B1
2 4 5 cDNA AR1-C1
2 4 6 cDNA AR3-C1
2 4 7 cDNA AR1-D1
2 4 8 cDNA AR3-D1
2 4 9 cDNA AR1-E1
2 4 10 cDNA AR3-E1
2 4 11 cDNA AR1-F1
2 4 12 cDNA AR3-F1
2 4 13 cDNA AR1-G1
2 4 14 cDNA AR3-G1
2 4 15 cDNA AR1-H1
2 4 16 cDNA AR3-H1
2 4 17 cDNA AR1-A7
2 4 18 cDNA AR3-A7
2 4 19 cDNA AR1-B7
2 4 20 cDNA AR3-B7
2 4 21 cDNA AR1-C7
2 4 22 cDNA AR3-C7
2 4 23 cDNA AR1-D7
2 4 24 cDNA AR3-D7
2 4 25 cDNA AR1-E7
2 4 26 cDNA AR3-E7
2 4 27 cDNA AR1-F7
2 4 28 cDNA AR3-F7
2 4 29 cDNA AR1-G7
2 4 30 cDNA AR3-G7
2 4 31 cDNA AR1-H7
2 4 32 cDNA AR3-H7
2 5 1 cDNA AR5-A1
2 5 2 cDNA SR1-A1
2 5 3 cDNA AR5-B1
2 5 4 cDNA SR1-B1
2 5 5 cDNA AR5-C1
2 5 6 cDNA SR1-C1
2 5 7 cDNA AR5-D1
2 5 8 cDNA SR1-D1
2 5 9 cDNA AR5-E1
2 5 10 cDNA SR1-E1
2 5 11 cDNA AR5-F1
2 5 12 cDNA SR1-F1
2 5 13 cDNA AR5-G1
2 5 14 cDNA SR1-G1
2 5 15 cDNA AR5-H1
2 5 16 cDNA SR1-H1
2 5 17 cDNA AR5-A7
2 5 18 cDNA SR1-A7
2 5 19 cDNA AR5-B7
2 5 20 cDNA SR1-B7
2 5 21 cDNA AR5-C7
2 5 22 cDNA SR1-C7
2 5 23 cDNA AR5-D7
2 5 24 cDNA SR1-D7
2 5 25 cDNA AR5-E7
2 5 26 cDNA SR1-E7
2 5 27 cDNA AR5-F7
2 5 28 cDNA SR1-F7
2 5 29 cDNA AR5-G7
2 5 30 cDNA SR1-G7
2 5 31 cDNA AR5-H7
2 5 32 cDNA SR1-H7
2 6 1 cDNA SR3-A1
2 6 2 cDNA SR5-A1
2 6 3 cDNA SR3-B1
2 6 4 cDNA SR5-B1
2 6 5 cDNA SR3-C1
2 6 6 cDNA SR5-C1
2 6 7 cDNA SR3-D1
2 6 8 cDNA SR5-D1
2 6 9 cDNA SR3-E1
2 6 10 cDNA SR5-E1
2 6 11 cDNA SR3-F1
2 6 12 cDNA SR5-F1
2 6 13 cDNA SR3-G1
2 6 14 cDNA SR5-G1
2 6 15 cDNA SR3-H1
2 6 16 cDNA SR5-H1
2 6 17 cDNA SR3-A7
2 6 18 cDNA SR5-A7
2 6 19 cDNA SR3-B7
2 6 20 cDNA SR5-B7
2 6 21 cDNA SR3-C7
2 6 22 cDNA SR5-C7
2 6 23 cDNA SR3-D7
2 6 24 cDNA SR5-D7
2 6 25 cDNA SR3-E7
2 6 26 cDNA SR5-E7
2 6 27 cDNA SR3-F7
2 6 28 cDNA SR5-F7
2 6 29 cDNA SR3-G7
2 6 30 cDNA SR5-G7
2 6 31 cDNA SR3-H7
2 6 32 cDNA SR5-H7
2 7 1 control CON_Bt
2 7 2 blank BLANK
2 7 3 control CON_GFP
2 7 4 blank BLANK
2 7 5 control CON_Globin
2 7 6 blank BLANK
2 7 7 control CON_GUS
2 7 8 blank BLANK
2 7 9 control CON_HPH
2 7 10 blank BLANK
2 7 11 control CON_Luc
2 7 12 blank BLANK
2 7 13 control CON_Bar
2 7 14 blank BLANK
2 7 15 control CON_nptII
2 7 16 blank BLANK
2 7 17 control CON_Sp1
2 7 18 blank BLANK
2 7 19 control CON_Sp2
2 7 20 blank BLANK
2 7 21 blank BLANK
2 7 22 blank BLANK
2 7 23 blank BLANK
2 7 24 blank BLANK
2 7 25 blank BLANK
2 7 26 blank BLANK
2 7 27 blank BLANK
2 7 28 blank BLANK
2 7 29 blank BLANK
2 7 30 blank BLANK
2 7 31 blank BLANK
2 7 32 blank BLANK

--
Dave Berger, PhD
Associate Professor, Botany
Room 6-26,Agricultural Sciences Building
Lynnwood Road
University of Pretoria, Pretoria, 0002, South Africa
Phone: +27-12-420 4634 / 4239   Fax:   +27-12-420 3947
http://www.up.ac.za/academic/botany/berger.html

SA "Tree of the Year" 2005
Adansonia digitata (Baobab)