Hello,
  An issue was reported when I was doing the following commands.
>library(limma)
>library(affy)
> eset.rma <- justRMA(celfile.path="/media/Computational
Science/Intern/cel")
> pData(eset.rma)
              sample
GSM194153.CEL      1
GSM194154.CEL      2
GSM194155.CEL      3
GSM194156.CEL      4
GSM194157.CEL      5
GSM194158.CEL      6
GSM194159.CEL      7
GSM194160.CEL      8
GSM194161.CEL      9
GSM194162.CEL     10
GSM194163.CEL     11
GSM194164.CEL     12
GSM194165.CEL     13
GSM194166.CEL     14
GSM194167.CEL     15
GSM194168.CEL     16
GSM194169.CEL     17
GSM194170.CEL     18
GSM194171.CEL     19
GSM194172.CEL     20
GSM194173.CEL     21
> a<-rep(0,length(pData(eset.rma)$sample))
> a[grep("control", rownames(pData(eset.rma)), ignore.case=T)] <-1
> a
 [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> design <- cbind(caregiver=1, controlVscaregiver=a)
> design
      caregiver controlVscaregiver
 [1,]         1                  0
 [2,]         1                  0
 [3,]         1                  0
 [4,]         1                  0
 [5,]         1                  0
 [6,]         1                  0
 [7,]         1                  0
 [8,]         1                  0
 [9,]         1                  0
[10,]         1                  0
[11,]         1                  0
[12,]         1                  0
[13,]         1                  0
[14,]         1                  0
[15,]         1                  0
[16,]         1                  0
[17,]         1                  0
[18,]         1                  0
[19,]         1                  0
[20,]         1                  0
[21,]         1                  0
> fit <- lmFit(eset.rma, design)
Coefficients not estimable: controlVscaregiver
Warning message:
Partial NA coefficients for 22283 probe(s)

Is this issue has reported because of the coefficients i have selected.
I don't know how to resolve this issue. Thanks in advance for any help.

-
*Laya Rose*

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