

Dear List,

This one of the hundreds of "how do I create a design matrix in limma question". However, I have difficulties in setting up a paired design, with some error messages I really do not understand. The experiment consists of 27 U133A arrays from 9 patients with 3 different conditions (2 diseases plus healthy controls). From each patient we have 3 different brain regions. I want to compare the difference between the brain regions in the different diseases. therefore I want to match the samples from the individual patients. I attached the code below. When I try to fit the model with lmFit I get following error message:

> fit <- lmFit(data.norm, design)
Coefficients not estimable: sample_881 sample_936 
Warning message:
In lmFit(data.norm, design) :
Some coefficients not estimable: coefficient interpretation may vary.

What I dont understand is why can I calculate the coefficients for all but 2 samples? I allready doublechecked my target file and design matrix and can't find any clue what might be wrong with these two samples, so any hint is highly appreciated.

Best Regards, 

Mike



Here is the code I used:

> target
File disease patient region
1 "Cbm 628 U133A.CEL" PD 628 Cerebellum
2 "Cbm 631 U133A.CEL" MSA 631 Cerebellum
3 "Cbm 650 U133A.CEL" PD 650 Cerebellum
4 "Cbm 755 U133A.CEL" PD 755 Cerebellum
5 "Cbm 758 U133A.CEL" Co 758 Cerebellum
6 "Cbm 769 U133A.CEL" MSA 769 Cerebellum
7 "Cbm 776 U133A.CEL" MSA 776 Cerebellum
8 "Cbm 881 U133A.CEL" MSA 881 Cerebellum
9 "Cbm 936 U133A.CEL" Co 936 Cerebellum
10 "E4R_042a12b.CEL" Co 936 Cortex
11 "I4R_012a1.CEL" PD 628 Cortex
12 "I4R_012a11.CEL" MSA 881 Cortex
13 "I4R_012a2.CEL" MSA 631 Cortex
14 "I4R_012a3.CEL" PD 650 Cortex
15 "I4R_012a6.CEL" PD 755 Cortex
16 "I4R_012a7.CEL" Co 758 Cortex
17 "I4R_012a8.CEL" MSA 769 Cortex
18 "I4R_012a9.CEL" MSA 776 Cortex
19 "pn0628_133a.CEL" PD 628 Putamen
20 "pn0631_133a.CEL" MSA 631 Putamen
21 "pn0650_133a.CEL" PD 650 Putamen
22 "pn0755_133a.CEL" PD 755 Putamen
23 "pn0758_133a.CEL" Co 758 Putamen
24 "pn0769_133a.CEL" MSA 769 Putamen
25 "pn0776_133a.CEL" MSA 776 Putamen
26 "pn0881_133a.CEL" MSA 881 Putamen
27 "pn0936_133a.CEL" Co 936 Putamen

> condition <- as.factor(paste(disease, rep(c("Cbm", "Cor", "Ptm"), each=9), sep="."))
> sample <- as.factor(paste("_", patient, sep=""))
> 
> design <- model.matrix(~0+condition+sample)
> colnames(design)[1:9] <- sort(as.character(unique(condition)))
> fit <- lmFit(data.norm, design)
Coefficients not estimable: sample_881 sample_936 
Warning message:
In lmFit(data.norm, design) :
 Some coefficients not estimable: coefficient interpretation may vary.
> sessionInfo()
R version 2.7.0 (2008-04-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252

attached base packages:
[1] tools stats graphics grDevices utils datasets methods 
[8] base 

other attached packages:
[1] affy_1.18.2 preprocessCore_1.2.0 affyio_1.8.0 
[4] Biobase_2.0.1 limma_2.14.5 

loaded via a namespace (and not attached):
[1] scatterplot3d_0.3-27
> 


-- 
Dr. Michael Walter

The Microarray Facility
University of Tuebingen
Calwerstr. 7
72076 Tübingen/GERMANY

Tel.: +49 (0) 7071 29 83210
Fax. + 49 (0) 7071 29 5228

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