[BioC] limma - dupcor.series

Helen Cattan helen.cattan at jenner.ac.uk
Sun Apr 18 21:01:15 CEST 2004


Hi,

Thanks for the reply. I've typed in what you suggested for more
information. Done with and without background correction. I don't know
what you are looking for - but hope this helps.


After using RG=backgroundCorrect(RG, method="minimum")

summary(MAmin2$M)
 QCmouse..CD4.depl.day.7..260803...590.530..liver.
 Min.   :0                                        
 1st Qu.:0                                        
 Median :0                                        
 Mean   :0                                        
 3rd Qu.:0                                        
 Max.   :0                                        
                                                  
 QCmouse..CD4.depl.day.8..10903.II....590.550..liver.4
 Min.   :0                                            
 1st Qu.:0                                            
 Median :0                                            
 Mean   :0                                            
 3rd Qu.:0                                            
 Max.   :0                                            
                                                      
 QCmouse.liver..CD4.depl..1.6.ug..day.8..670.530..240703
 Min.   :0                                              
 1st Qu.:0                                              
 Median :0                                              
 Mean   :0                                              
 3rd Qu.:0                                              
 Max.   :0                                              
                                                        
 QCmouse.liver.CD4.depl.day.8..10903.I....590.540..
 Min.   :   NA                                     
 1st Qu.:   NA                                     
 Median :   NA                                     
 Mean   :  NaN                                     
 3rd Qu.:   NA                                     
 Max.   :   NA                                     
 NA's   :31200                                     
>
summary(MAmin2$weights)
QCmouse..CD4.depl.day.7..260803...590.530..liver.
 Min.   :0.0000                                   
 1st Qu.:1.0000                                   
 Median :1.0000                                   
 Mean   :0.9873                                   
 3rd Qu.:1.0000                                   
 Max.   :1.0000                                   
 QCmouse..CD4.depl.day.8..10903.II....590.550..liver.4
 Min.   :0.000                                        
 1st Qu.:1.000                                        
 Median :1.000                                        
 Mean   :0.986                                        
 3rd Qu.:1.000                                        
 Max.   :1.000                                        
 QCmouse.liver..CD4.depl..1.6.ug..day.8..670.530..240703
 Min.   :0.0000                                         
 1st Qu.:1.0000                                         
 Median :1.0000                                         
 Mean   :0.9762                                         
 3rd Qu.:1.0000                                         
 Max.   :1.0000                                         
 QCmouse.liver.CD4.depl.day.8..10903.I....590.540..
 Min.   :0.0000                                    
 1st Qu.:1.0000                                    
 Median :1.0000                                    
 Mean   :0.9878                                    
 3rd Qu.:1.0000                                    
 Max.   :1.0000                                    
>
> summary(cor$cor.genes)
Length  Class   Mode 
     0   NULL   NULL 
>
And not using background correct

> summary(MA1$M)
 QCmouse..CD4.depl.day.7..260803...590.530..liver.
 Min.   :-5.188e+00                               
 1st Qu.:-2.813e-01                               
 Median :-1.425e-02                               
 Mean   : 2.424e-02                               
 3rd Qu.: 2.949e-01                               
 Max.   : 5.752e+00                               
 NA's   : 1.326e+04                               
 QCmouse..CD4.depl.day.8..10903.II....590.550..liver.4
 Min.   :  -5.25729                                   
 1st Qu.:  -0.24996                                   
 Median :  -0.03117                                   
 Mean   :   0.09563                                   
 3rd Qu.:   0.35874                                   
 Max.   :   6.01569                                   
 NA's   :8209.00000                                   
 QCmouse.liver..CD4.depl..1.6.ug..day.8..670.530..240703
 Min.   :-7.200e+00                                     
 1st Qu.:-2.703e-01                                     
 Median : 4.189e-03                                     
 Mean   : 3.571e-02                                     
 3rd Qu.: 3.068e-01                                     
 Max.   : 1.293e+01                                     
 NA's   : 1.611e+04                                     
 QCmouse.liver.CD4.depl.day.8..10903.I....590.540..
 Min.   :-7.880e+00                                
 1st Qu.:-2.729e-01                                
 Median :-5.434e-04                                
 Mean   : 8.506e-02                                
 3rd Qu.: 3.162e-01                                
 Max.   : 1.025e+01                                
 NA's   : 1.808e+04                                
>

> summary(MA1$weights)
 QCmouse..CD4.depl.day.7..260803...590.530..liver.
 Min.   :0.0000                                   
 1st Qu.:1.0000                                   
 Median :1.0000                                   
 Mean   :0.9873                                   
 3rd Qu.:1.0000                                   
 Max.   :1.0000                                   
 QCmouse..CD4.depl.day.8..10903.II....590.550..liver.4
 Min.   :0.000                                        
 1st Qu.:1.000                                        
 Median :1.000                                        
 Mean   :0.986                                        
 3rd Qu.:1.000                                        
 Max.   :1.000                                        
 QCmouse.liver..CD4.depl..1.6.ug..day.8..670.530..240703
 Min.   :0.0000                                         
 1st Qu.:1.0000                                         
 Median :1.0000                                         
 Mean   :0.9762                                         
 3rd Qu.:1.0000                                         
 Max.   :1.0000                                         
 QCmouse.liver.CD4.depl.day.8..10903.I....590.540..
 Min.   :0.0000                                    
 1st Qu.:1.0000                                    
 Median :1.0000                                    
 Mean   :0.9878                                    
 3rd Qu.:1.0000                                    
 Max.   :1.0000                                    
>
> summary(cor$cor.genes)
Length  Class   Mode 
     0   NULL   NULL



Thanks,
Helen

-----Original Message-----
From: Gordon Smyth [mailto:smyth at wehi.edu.au] 
Sent: 16 April 2004 00:18
To: Helen Cattan
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] limma - dupcor.series

At 01:59 AM 16/04/2004, Helen Cattan wrote:
>Hi,
>
>-using Bioconductor v1.8.1 and limma v1.6.1
>When I use backgroundCorrect(minimum) and then dupcor.series I don't
get
>a correlation value (NaN), if I don't use the backgroundCorrect method
I
>get a value but with a warning message. Does anyone have any
suggestions
>as to what is happening here and how I can sort it out please? (I
>realize the experimental design is hopeless but I have to work with
what
>I'm given). I don't have any missing/blank values but obviously have
>negative values after background subtraction. Code and warning are
given
>below.
>Thanks,
>
>Helen
>
> > files=dir(pattern="*\\.gpr")
> > RG=read.maimages(files, columns=list(Rf="F635 Median", Gf="F532
>Median", Rb="B635 Median", Gb="B532 Median"), wt.fun=wtflags(0))
> > names(RG)
> > RG$genes=readGAL()
> > RG$printer=getLayout(RG$genes)
> > samples=read.table("sampleinformationa.txt", header=TRUE, sep="\t",
>as.is=TRUE)
> > samples
> > spottypes=readSpotTypes()
> > RG$genes$Status=controlStatus(spottypes, RG)
> > RGmin=backgroundCorrect(RG, method="minimum")
> > MAmin=normalizeWithinArrays(RGmin, RG$printer)

No need to type 'RG$printer', the function will find it automatically.

> > MAmin2=normalizeBetweenArrays(MAmin)
> > design=c(1,1,1,1)
> > cor=dupcor.series(MAmin2$M, design, ndups=2, spacing=1)
>Loading required package: statmod
>
>Attaching package 'statmod':
>
>
>         The following object(s) are masked from package:limma :
>
>          matvec vecmat
>
> > cor$cor
>[1] NaN

I don't know what the problem is, presumably it is a problem with 
method="minimum". Can you please type summary(MAmin2$M), 
summary(MAmin2$weights) and summary(cor$cor.genes) to give more
information?

> > MAdef=normalizeWithinArrays(RG, RG$printer)
> > MAdef2=normalizeBetweenArrays(MAdef)
> > design=c(1,1,1,1)
> > cor=dupcor.series(MAdef2$M, design, ndups=2, spacing=1)
>Warning messages:
>1: Too much damping - convergence tolerance not achievable in:
>glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
>trace)
>2: Too much damping - convergence tolerance not achievable in:
>glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
>trace)
>3: Too much damping - convergence tolerance not achievable in:
>glmgam.fit(dx, dy, start = start, tol = tol, maxit = maxit, trace =
>trace)
>[1] 0.7891024

The warnings are no problem.

Gordon



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