[BioC] marrayQuality & marray : empty ?

[Paquet, Agnes]

Hi,

marray is using a reference table named controlCode to check the control
status of the spotted probes. controlCode is a matrix with 2 columns
named: Pattern and Name. You can check the default controlCode by typing
in R:
library(marray)
controlCode

   Pattern      Name      
1  "Buffer"     "Buffer"  
2  "Empty"      "Empty"   
3  "EMPTY"      "Empty"   
4  "AT"         "Negative"
5  "NC"         "Negative"
6  "M200009348" "Positive"
7  "M200012700" "Positive"
8

To specify your own controls, you have to create your own controlCode
matrix. This can be done by either using the readcontrolCode function in
marray or by reading a tab-delimited text file directly.

controlCode <- as.matrix(read.table("mycontrolCode.txt",
sep="\t",header=TRUE, quote="\"", fill=TRUE)))

Then, you can fill up the maControls slot by calling the function
maGenControls.
It is easier to use read.Galfile instead of read.marrayLayout and
read.marrayInfo to read your array information. You will need to add
your control column name in the info.id argument:

Assume mraw is a marrayRaw object:
test <- read.Galfile(info.id = c("ID", "Name", "ctl"))
maLayout(mraw) <- test$layout
maGnames(mraw) <- test$gnames

Then, you can define your controls using the function maGenControls,
specifying your control column in the id argument:
maControls(mraw) <- maGenControls(Gnames, controlcode=newControlCode, id
= "correctCtlID")


Regards,

Agnes




-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Ghislaine
Guigon
Sent: Tuesday, March 01, 2005 4:46 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] marrayQuality & marray : empty ?

hi,

I have a control column : "ctl" in gal file with control information,
and I 
define maLayout like this :
         manip.layout <- 
read.marrayLayout(fname=file.gal,ngr=ngr,ngc=ngc,nsr=nsr,nsc=nsc,skip=sk
ip, 
ctl.col = "ctl")
         x <-  as.character(maInfo(manip.gnames)[,"ctl"])
         y <- rep("probes", maNspots(manip.layout))
         y[x == "control"] <- "control"
         slot(manip.layout, "maControls") <- as.factor(y)

By this way, fonction maQualityPlots from the marrayQuality package
creates 
DotPlots with control spots (in green) but not with empty spots.

How and where empty spots are they defined in the marray format ?

thanks

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