Entering edit mode
Dear Juan Lin,
Only one of your samples has a technical replicate, and this is not
enough
information to estimate the duplicate (within sample) correlation, so
you
can't use the duplicateCorrelation() function. You need to either
average
the two technical replicates (there is a function avearrays in the
developmental version of limma for this purpose), or just choose the
technical replicate that looks of highest quality and drop the other
one.
Best wishes
Gordon
> Date: Fri, 24 Sep 2010 15:17:28 -0400
> From: "Juan Lin" <julin at="" aecom.yu.edu="">
> To: <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] unbalanced block design using limma
> Message-ID: <002801cb5c1d$20f9cd40$62ed67c0$@yu.edu>
> Content-Type: text/plain
>
> Dear List,
>
>
>
> I am using limma to analyze a affy ST1.0 dataset.
>
>
>
> I have 6 patients from which I have two tissue types: tumor and non-
tumor.
> One of the sample has a technical repeat, resulting 12 arrays.
>
> I would like to compare tumor vs. non-tumor and incorporate the
pairing and
> technical repeats information into the analysis. However, I got
error when I
> tried to calculate the correlation using duplicatedCorrelation
> function(please see code below). Therefore, I cannot do limma fit as
usual.
>
>
>
>> library(limma)
>
>> target<-read.table("target.txt",header=T,sep="\t")
>
>
>
>> target
>
> FileName Type Tumor Patient Repeat
>
> 1 8671-596NT.CEL ADENO N 1 1
>
> 2 8672-543T.CEL ADENO Y 2 2
>
> 3 8674-558T.CEL ADENO Y 3 3
>
> 4 8675-558NT.CEL ADENO N 3 4
>
> 5 8676-560T.CEL ADENO Y 4 5
>
> 6 8677-560NT.CEL ADENO N 4 6
>
> 7 8679-596NT2.CEL ADENO N 1 1
>
> 8 8686-507T.CEL ADENO Y 5 7
>
> 9 8687-507NT.CEL ADENO N 5 8
>
> 10 8688-507NTb.CEL ADENO N 5 9
>
> 11 8689-538T.CEL ADENO Y 6 10
>
> 12 8690-538NT.CEL ADENO N 6 11
>
>
>
>> F<-factor(target$Tumor,levels=c("N","Y"))
>
>> Patient<-factor(target$Patient)
>
>> design<-model.matrix(~Patient+F)
>
>> design
>
> (Intercept) Patient2 Patient3 Patient4 Patient5 Patient6 FY
>
> 1 1 0 0 0 0 0 0
>
> 2 1 1 0 0 0 0 1
>
> 3 1 0 1 0 0 0 1
>
> 4 1 0 1 0 0 0 0
>
> 5 1 0 0 1 0 0 1
>
> 6 1 0 0 1 0 0 0
>
> 7 1 0 0 0 0 0 0
>
> 8 1 0 0 0 1 0 1
>
> 9 1 0 0 0 1 0 0
>
> 10 1 0 0 0 1 0 0
>
> 11 1 0 0 0 0 1 1
>
> 12 1 0 0 0 0 1 0
>
>
>
>> corfit<-duplicateCorrelation(intensity,design,ndups=1,block=target$
Repeat)
>
> Loading required package: statmod
>
>
>
>>
fit<-lmFit(intensity,design,block=target$Repeat,cor=corfit$consensus)
>
> Error in backsolve(cholV, t(M), transpose = TRUE) :
>
> NA/NaN/Inf in foreign function call (arg 1)fit<-eBayes(fit)
>
>
>
> Hope someone can help me to figure out the problem . Thanks!
>
>
>
> Juan Lin
>
> AECOM
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