[BioC] errors with imageplot3by2

[alison waller]

Hi all,

I'm having getting confused with the imagebplot3by2 command.  
I am able to use imageplot to plot (R,G, Rb, log2R etc.) for the individual
arrays, but I cannot use imageplot3by2.  I'm not sure if I am using the
incorrect syntax or if there is an error in my data that is making this
function impossible.

I've pasted all my attempts below.  If anyone can help interpret the error
messages that would be great. I think that the na.rm=TRUE is telling me
something about missing values, and I'm not too sure about c(0.05,0.95).
This is some vector c, and specific values?

Thanks,

Alison


> library(limma)
> targets<-readTargets("VCMeOHTargets.txt")
> RG<-read.maimages(targets$FileName,source='genepix')
Read 830scan3.gpr 
Read 778scan2.gpr 
Read 784scan2.gpr 
Read 729Sscan2.gpr 
Read 797scan2bckp.gpr 
Read 791scan2bckp.gpr 
> plot (log2(RG$G[,1]),log2(RG$R[,1]))
> imageplot3by2(log2(RG$R),low='white',hig='red')
Error in RG[[z]] : subscript out of bounds
> RG.b<-backgroundCorrect(RG,method='minimum')
> dim(RG$R)
[1] 19200     6
> imageplot(log2(RG$R[,1]),RG$printer,low='white',high='red')
> RG
An object of class "RGList"
$R
     830scan3 778scan2 784scan2 729Sscan2 797scan2bckp 791scan2bckp
[1,]       94       73       88       122          113          106
[2,]    10133    12009    17661     17656         7191        11029
[3,]       31       30       45        53           67           33
[4,]       45       34       44        54           60           33
[5,]      177      107      134       209           86          131
19195 more rows ...

$G
     830scan3 778scan2 784scan2 729Sscan2 797scan2bckp 791scan2bckp
[1,]       96       87      106       101          125          100
[2,]     8720     9383     8453     13508         5462         6119
[3,]       33       34       46        49           89           36
[4,]       51       37       44        48           90           38
[5,]      124       86       99       143          122           98
19195 more rows ...

$Rb
     830scan3 778scan2 784scan2 729Sscan2 797scan2bckp 791scan2bckp
[1,]       27       25       54        53           63           32
[2,]       26       26       40        54           63           32
[3,]       25       24       36        47           64           28
[4,]       25       24       37        47           61           26
[5,]       25       25       41        53           52           26
19195 more rows ...

$Gb
     830scan3 778scan2 784scan2 729Sscan2 797scan2bckp 791scan2bckp
[1,]       27       26       88        38           92           35
[2,]       29       28       48        39           94           33
[3,]       26       27       41        37           92           30
[4,]       26       28       40        41           83           29
[5,]       25       27       51        49           69           29
19195 more rows ...

$targets
                     FileName
830scan3         830scan3.gpr
778scan2         778scan2.gpr
784scan2         784scan2.gpr
729Sscan2       729Sscan2.gpr
797scan2bckp 797scan2bckp.gpr
791scan2bckp 791scan2bckp.gpr

$genes
  Block Row Column    ID         Name
1     1   1      1 03H13 Kbgs-005-H13
2     1   1      2 03H01  Kbgs-005-H1
3     1   1      3 03D13 Kbgs-005-D13
4     1   1      4 03D01  Kbgs-005-D1
5     1   1      5 02P13 Kbgs-004-P13
19195 more rows ...

$source
[1] "genepix"

$printer
$ngrid.r
[1] 12

$ngrid.c
[1] 4

$nspot.r
[1] 20

$nspot.c
[1] 20

$ndups
[1] 1

$spacing
[1] 1

attr(,"class")
[1] "PrintLayout"

> imageplot3by2(RG,RG$R,low='white',high='red',common.lim=TRUE)
Error in quantile(RG[[z]], c(0.05, 0.95), na.rm = TRUE) : 
        no such index at level 1
> z<-RG
> imageplot3by2(RG,z=RG$R,zlim=NULL,common.lim=TRUE)
Error in quantile(RG[[z]], c(0.05, 0.95), na.rm = TRUE) : 
        no such index at level 1