[BioC] LIMMA package - coefficient not estimable

[Sean Davis]

On Fri, Mar 30, 2012 at 8:24 AM, yeeling chong <yeelingchong at gmail.com> wrote:
> Thanks Sean,
>
>  I tried to remove the third replicate before and it can estimate both
> biorep1 & 2 coefficients. How does this correlate with the degree of
> freedom then? Thanks again.

Removing a parameter from the fit increases the DOF by 1.

http://en.wikipedia.org/wiki/Degrees_of_freedom_(statistics)

Sean

>
> On Fri, Mar 30, 2012 at 8:17 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> On Fri, Mar 30, 2012 at 8:09 AM, yeeling chong <yeelingchong at gmail.com> wrote:
>>> Dear Lists,
>>>
>>> I'm currently using LIMMA package to analyze my microarray datasets.
>>> For each treatment, I have three biological replicates. The subset of
>>> the constructed design look like this:
>>> Array
>>> R16A    R16B    R16C    R16D    R16E    S03A      ------   Biorep1      Biorep2 Biorep3
>>> 02152012_462157_A01_1613_cy5_R16E       0       0       0       0       1       0       ------ 1        0       0
>>> 02152012_462157_A01_161_cy3_R16A        1       0       0       0       0       0       ------ 1        0       0
>>> 02152012_462157_A02_81_cy5_R08A         0       0       0       0       0       0       ------ 0        0
>>> 02152012_462157_A02_813_cy3_R08E        0       0       0       0       0       0       ------ 1        0       0
>>> 02152012_462157_A03_164_cy5_R16B        0       1       0       0       0       0       ------ 1        0       0
>>> 02152012_462157_A03_1614_cy3_R16E       0       0       0       0       1       0       ------ 0        1       0
>>> 02152012_462157_A04_89_cy5_R08C 0       0       0       0       0       0       0       ------ 0        1
>>> 02152012_462157_A04_811_cy3_R08D        0       0       0       0       0       0       ------ 0        1       0
>>> 02152012_462157_A05_1611_cy5_R16D       0       0       0       1       0       0       ------ 0        1       0
>>>
>>> When I fit my data into lmFit, it doesn't estimate the coefficient of
>>> the third biological replicates. The error msg looks like this:
>>>
>>>> Fit=lmFit(norm.dataM,designlm,correlation=corfit$consensus)
>>> Coefficients not estimable: Biorep3
>>> Warning message:
>>> Partial NA coefficients for 22664 probe(s)
>>
>> The coefficients not estimable means that you do not have enough
>> degrees of freedom given your number of samples and number of effects
>> you are trying to estimate.  In the normal use case, one does not
>> include the BiorepX columns in the design matrix.  I'd suggest
>> removing the Bioreps columns from the design matrix (unless you really
>> are interested in the biological replicates).
>>
>> Sean
>>
>>
>>
>>> Can anyone tell me what's goes wrong my my design? Thanks a lot
>>>
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