[BioC] Error:"arrayQuality"

[Paquet, Agnes]

Hi,

This error occurs when spot types (e.g. positive controls, negative
controls...) are not set up properly in the RGlist or marrayRaw object
and/or the spot type's look-up table named controlCode is not matching
the various spot types on the array.

The spot types used in arrayQuality are defined in a 2 column matrix
called controlCode. By default, it is set to the various types of
controls we use in the Genomics Core at UCSF. You can see the default
values in controlCode by typing in R:
> controlCode
   Pattern      Name      
1  "Buffer"     "Buffer"  
2  "Empty"      "Empty"   
3  "EMPTY"      "Empty"   
4  "AT"         "Negative"
5  "NC"         "Negative"
6

- To define spot types in your RGlist object:
The easiest way to do it is to create a tab-delimited text file named
SpotTypes.txt. You can find more explanations about SpotType files and
how to set up your controls in your RGlist object in the limma User's
Guide.


- To define your own spot type's look-up table:
You will need to replace the default values in controlCode with your
values. You should be able to use the same SpotType file for this step.
You can read it into arrayQuality using the function readcontrolCode. It
is also possible to create a new controlCode matrix directly. More
details for this step are provided in the last section of arrayQuality
user's guide.

controlCode <- readcontrolCode(file="mySpotTypes.txt", controlId="ID")

Please let me know if you have any more problems.

Best,

Agnes


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Khan,
Sohail
Sent: Friday, September 30, 2005 9:14 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Error:"arrayQuality"

Dear Members,

In regards to my previous question here is my session out.


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> library(arrayQuality)
Loading required package: marray
Loading required package: limma
Loading required package: convert
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor 
         Vignettes contain introductory material.  To view, 
         simply type: openVignette() 
         For details on reading vignettes, see
         the openVignette help page.
[1] "arrayQuality"
[1] "Checking for missing packages"
Garbage collection 60 = 53+4+3 (level 2) ... 
102028 cons cells free (21%)
5.0 Mbytes of heap free (84%)
[1] "Loading required packages"

Attaching package: 'mclust'


        The following object(s) are masked from package:stats :

         density 

Warning message:
package 'marray' was built under R version 2.2.0 
> files<-c("43.gpr","48.gpr","93.gpr","95.gpr")
> files
[1] "43.gpr" "48.gpr" "93.gpr" "95.gpr"
> RG<-read.maimages(files,source="genepix")
Read 43.gpr 
Read 48.gpr 
Read 93.gpr 
Read 95.gpr 
> results<-maQualityPlots(RG)
Loading required package: hexbin
Loading required package: grid
Loading required package: colorspace

Attaching package: 'colorspace'


        The following object(s) are masked from package:grDevices :

         hcl 

Error in if (is.int(totalPlate)) { : argument is of length zero

Sohail Khan
Scientific Programmer
COLD SPRING HARBOR LABORATORY
Genome Research Center
500 Sunnyside Boulevard
Woodbury, NY 11797
(516)422-4076

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