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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