Hi Jose,
 
Thanks. 
 Each array is 4 by 4 sub-grids (pins) each with 21 by 22 spots. The genelist.dat file (an external file for the gene array list) contains header GRID  ROW  COL and ID. When I tried to get the layout, the number of rows for the spot did not match. 
   
  x <- 1:16; c1 <- c(); for(i in x) c1 <- c(c1, rep(i, times=462)); 
   x <- 1:22; c2 <- c(); for(i in x) c2 <- c(c2, rep(i, times=21));
   c3 <- rep(1:22, times=21); 
   gnames<-read.table("genelist.dat", sep="\t", header=T)
  RG$genes <- data.frame(Block=c1, Row=rep(c2, times=16), 
  Column=rep(c3, times=16),ID=gnames$ID)
  RG$printer <- getLayout(RG$genes)
 RG$printer 
$ngrid.r
[1] 4
$ngrid.c
[1] 4
$nspot.r
[1] 22
$nspot.c
[1] 22
attr(,"class")
[1] "PrintLayout"
 nrow(RG$genes)
[1] 7392
ncol(RG$genes)
[1] 4
nrow(RG)
[1] 7392


I appreciate your help.Yolande


________________________________

From: bioconductor-bounces@stat.math.ethz.ch on behalf of J.delasHeras@ed.ac.uk
Sent: Fri 8/4/2006 8:49 AM
To: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] exclude flagged spots in limma



Quoting Yolande Tra <yvtsma@rit.edu>:

> Hi Jose,
>
> Thank you for your reply. One problem is that value of 1 was assigned
> for bad spots and 0 for good ones. Is there a way to switch these
> values?
>
> Yolande

Of course you can switch them.

If you already made a matrix from your flags (oldmatrix), and contain
ONLY the value 0 or
1, and you want to switch them over... just do this:

newmatrix<-abs(oldmatrix-1)

done.

If you have other values then you may want to use the 'if else' clauses
within a loop
('for') checking every element of the matrix, and then you can specify
what values to
substitute for... if you have a problem with this just shout.


Jose

--
Dr. Jose I. de las Heras                      Email: J.delasHeras@ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK

_______________________________________________
Bioconductor mailing list
Bioconductor@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor



	[[alternative HTML version deleted]]

