Hi Laya,

Please don't take things off list.

I would highly recommend reading the limma user's guide, which has examples
that show exactly what you should be doing here. But note that it is simple
to create the design matrix using the model.matrix() function:

design <- model.matrix(~factor(rep(1:2, c(11,10)))
colnames(design) <- c("caregiver","caregivervscontrol")

Best,

Jim


On Thu, Mar 14, 2013 at 2:17 AM, Laya Rose <roselaya98@gmail.com> wrote:

> Sir
>  Thank you for your reply. Actually R/Bioconductor is new to me. So very
> difficult for me to sort out the errors. Because of that i can't able to
> move on to next step. Files from GSM194164.CEL to GSM194173.CEL are the
> samples of control. Then how can the issue of no controls in the rownames
> of phenodata can occur.
>
> On Thu, Mar 14, 2013 at 2:02 AM, James W. MacDonald <jmacdon@uw.edu>wrote:
>
>> 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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>>>
>>
>>
>
>
> --
> *Laya Rose*
>
>

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