Hello List,
I am just forwarding Lorenzo's response to the list as he forgot to copy the
list. May be, this is of use in the future.

I think, your design is a unbalanced randomized incomplete block design, so
it doesn't matter if you have one treatment or multiple for a single block.
Also, the duplicateCorrelation is estimated from the data and the estimate
(0.1313324) being high or low doesn't come into the picture. The data
determines this for you, even if it seems that the data from the same mother
should be "more correlated". This may happen because of multiple reasons:
- May be the treatments are not dependent on the mother
- If the treatments are dependent, may be the relation between them is not
normal which leads to bad estimate of correlation.

and .. several similar reasons ..

Bottom line: If you trust the model, the data tells you that 0.1313324 is
the estimate of correlation between observations in a block. If you are not
happy with the estimate of correlation, probably try fitting a different
model.

Thanks,
S.

On Wed, Oct 6, 2010 at 7:30 PM, Lorenzo Bomba <lory.bomb@gmail.com> wrote:

>
>
> Hi Sunny,
>
> Thank you for the suggestions, I tried to use duplicate correlation as
> follow:
>
> TS <-target$Treatment
> design <- model.matrix(~-1+TS)
> colnames(design) <- levels(TS)
> block <- c(1,2,3,4,2,3,3,5,5,3,6,6)
> dupcor <- duplicateCorrelation(RDE,design,block=block)
>
>
> and the value of dupcor$consensus.correlation is 0.1313324.... really low
> for a average correlation.
> I could go on with the analysis? as you can see in the block I have some
> array correlated 'cause the same mother and other that are independent
> without duplicate....
> some other suggestions please??
>
>  Thank a lot for your effort!
>
> Cheers
>
> Lorenzo
>
> On 6 Oct 2010, at 20:50, Sunny Srivastava wrote:
>
> Hello Lorenzo,
> I am not sure if I understand your question correctly, but here is my
> $0.02.
>
> If you want to account for effect of mother, it would be better include it
> in your regression model as a factor, but I guess your aim is to detect the
> difference between DR and NODR (right?). If I understand you correctly (ie
> you are interested in NODR vs DR comparison), you probably want to model
> mothers as blocks. The duplicateCorrelation option in limma might come in
> handy in this case.
>
> Thanks,
> S.
>
> On Wed, Oct 6, 2010 at 12:56 PM, Lorenzo Bomba <lory.bomb@gmail.com>wrote:
>
>> Dear all,
>>
>> I have a conceptual problem with the "makeContrast"  function in Limma:
>> doing  a factorial design and the follow are the  targetfile and the
>> design matrix
>>
>> targetfile
>>
>> FileName        Scrofa  Treatment
>> S10M    S127    DR
>> S11     S52     DR
>> S12     S304    DR
>> S13     S9      NODR
>> S14     S52     DR
>> S15     S304    DR
>> S17rt   S304    DR
>> S18     S66     DR
>> S19     S66     NODR
>> S20     S304    NODR
>> S21     S93     NODR
>> S22     S93     NODR
>>
>>
>> > design
>>   S127.DR S304.DR S304.NODR S52.DR S66.DR S66.NODR S9.NODR S93.NODR
>> 1        1       0         0      0      0        0       0        0
>> 2        0       0         0      1      0        0       0        0
>> 3        0       1         0      0      0        0       0        0
>> 4        0       0         0      0      0        0       1        0
>> 5        0       0         0      1      0        0       0        0
>> 6        0       1         0      0      0        0       0        0
>> 7        0       1         0      0      0        0       0        0
>> 8        0       0         0      0      1        0       0        0
>> 9        0       0         0      0      0        1       0        0
>> 10       0       0         1      0      0        0       0        0
>> 11       0       0         0      0      0        0       0        1
>> 12       0       0         0      0      0        0       0        1
>> attr(,"assign")
>> [1] 1 1 1 1 1 1 1 1
>> attr(,"contrasts")
>> attr(,"contrasts")$TS
>> [1] "contr.treatment"
>>
>> I want see the difference between the NODR and the DR group taking in
>> account that they belong to different mothers ( S127   S304  .....etc ). How
>> can I set the makeContrast....
>> I tried  in this two ways.... but I don't know the difference between the
>> first and the second
>>
>> 1)cont.matrix <- makeContrasts(
>> DRvsNODR=(S127.DR+S304.DR+S52.DR)-(S304.NODR+S66.NODR+S9.NODR+S93.NODR),
>> levels=design)
>>
>> 2) cont.matrix <- makeContrasts(
>> DRvsNODR=(S127.DR-S304.DR-S52.DR)-(S304.NODR-S66.NODR-S9.NODR-S93.NODR),
>> levels=design)
>>
>> Could you help me please???
>>
>> Thanks in advance!
>>
>> Lorenzo
>>
>>
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>

	[[alternative HTML version deleted]]

