[BioC] issue when doing program.

[James W. MacDonald]

Hi Laya,


On 3/13/13 4:40 AM, Laya Rose wrote:
> 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

There are no controls in the row.names of your phenoData, so you are 
getting all zeros. You need to fix this step so you have a 1 for each 
control.

Best,

Jim


>> 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*
>
> 	[[alternative HTML version deleted]]
>
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