[BioC] limma: duplicates handling

[Andres Pinzon]

Hi Jenny, you are completely right.
Im going through the ?avedups documentation right now.

Thank you.

Best,



On Wed, Apr 22, 2009 at 11:53 AM, Jenny Drnevich <drnevich at illinois.edu> wrote:
> Hi Andres,
>
> Did you read through the help file for duplicateCorrelation? You can't do
> both block and ndups:
>
> "At this time it is not possible to estimate correlations between duplicate
> spots and between technical replicates simultaneously. If block is not null,
> then the function will set ndups=1."
>
> If you have a blocking variable and technical replicates, you cannot use
> limma to adjust for both. What to do in this situation has been discussed
> previously on this list many times; see:
> https://stat.ethz.ch/pipermail/bioconductor/2008-November/025116.html
>
> HTH,
> Jenny
>
>
> At 08:40 AM 4/22/2009, Andres Pinzon wrote:
>>
>> Hi Jenny,
>> Thanks for the advice. This is the part of the  code I think is not
>> working:
>> ===
>> +
>> +>biolrep <- c(1,1,2,2,3,3)
>> +>corfit <- duplicateCorrelation(MA,ndups=2,block=biolrep, spacing=8)
>> +>fit <- lmFit (MA, block=biolrep, cor=corfit$consensus)
>> +>fit <- eBayes(fit)
>> +
>> ===
>>
>> Shoudl I  use something like?:
>>
>> fit <- lmFit (MA, block=biolrep, ndups=2, spacing=8, cor=corfit$consensus)
>>
>>
>>
>> best,
>>
>>
>> On Wed, Apr 22, 2009 at 9:21 AM, Jenny Drnevich <drnevich at illinois.edu>
>> wrote:
>> > Hi Andres and Jim,
>> >
>> > Actually, there is a way that limma accounts for the duplicates and only
>> > reports one value per clone in topTable. Did you follow the Within-Array
>> > Replicate Spot example 11.6 in the limmaUsersGuide()? After you use
>> > duplicateCorrelation() to calculate the correlation between spots, you
>> > have
>> > to modify the call to lmFit:
>> >
>> > fit <- lmFit(MA2, design, ndups=2, correlation=corfit$consensus)
>> >
>> > Andres - in the future, it would help if you posted your code that
>> > wasn't
>> > working along with the output of sessionInfo() so we could see what
>> > exactly
>> > you did and what you need to do.
>> >
>> > Cheers,
>> > Jenny
>> >
>> > At 07:59 AM 4/22/2009, James W. MacDonald wrote:
>> >>
>> >> Hi Andres,
>> >>
>> >> Andres Pinzon wrote:
>> >>>
>> >>> Hi James!
>> >>> On Wed, Apr 22, 2009 at 8:40 AM, James W. MacDonald
>> >>> <jmacdon at med.umich.edu> wrote:
>> >>>>
>> >>>> Hi Andres,
>> >>>>
>> >>>> Andres Pinzon wrote:
>> >>>>>
>> >>>>> Hi Everyone,
>> >>>>>
>> >>>>> If I have duplicates in each slide of my experiment, how do I tell
>> >>>>> limma
>> >>>>> to handle this?
>> >>>>> I am using duplicateCorrelation() function, but after the whole
>> >>>>> process
>> >>>>> the topTable() reports not half of the spots but all of them,
>> >>>>> For instance, if there are overall 15000 spots in my experiment, and
>> >>>>> half of them are
>> >>>>> duplicates, Shouldn't I end up just with 7500 genes?
>> >>>>
>> >>>> Nope. When you use duplicateCorrelation() you are telling limma to
>> >>>> fit a
>> >>>> mixed model that accounts for correlation between duplicate spots.
>> >>>> But
>> >>>> you
>> >>>> are not telling limma to take averages and just report one value.
>> >>>
>> >>> Ok, thanks for answering. Any idea on how to tell limma to take
>> >>> average and report just one value?
>> >>> Sorry I really can not figure it out.
>> >>
>> >> I don't think there are facilities within limma to do this. If this is
>> >> what you want to do, then you should just compute the averages and then
>> >> fit
>> >> the model using the averages.
>> >>
>> >>
>> >>> Best,
>> >>
>> >> --
>> >> James W. MacDonald, M.S.
>> >> Biostatistician
>> >> Douglas Lab
>> >> University of Michigan
>> >> Department of Human Genetics
>> >> 5912 Buhl
>> >> 1241 E. Catherine St.
>> >> Ann Arbor MI 48109-5618
>> >> 734-615-7826
>> >>
>> >> _______________________________________________
>> >> Bioconductor mailing list
>> >> Bioconductor at stat.math.ethz.ch
>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> Search the archives:
>> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> > Jenny Drnevich, Ph.D.
>> >
>> > Functional Genomics Bioinformatics Specialist
>> > W.M. Keck Center for Comparative and Functional Genomics
>> > Roy J. Carver Biotechnology Center
>> > University of Illinois, Urbana-Champaign
>> >
>> > 330 ERML
>> > 1201 W. Gregory Dr.
>> > Urbana, IL 61801
>> > USA
>> >
>> > ph: 217-244-7355
>> > fax: 217-265-5066
>> > e-mail: drnevich at illinois.edu
>> >
>>
>>
>>
>> --
>> Andrés Pinzón
>> http://bioinf.ibun.unal.edu.co/~apinzon/
>> Bioinformatics Center, Colombia EMBnet node
>> http://bioinf.ibun.unal.edu.co
>> Tel +57 3165000 ext 16961 Fax +571 3165415
>> Micology and Phytopathology Laboratory - Los Andes University.
>> http://bioinf.uniandes.edu.co
>> Tel +571 3394949 ext. 2768
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu
>



-- 
Andrés Pinzón
http://bioinf.ibun.unal.edu.co/~apinzon/
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
http://bioinf.uniandes.edu.co
Tel +571 3394949 ext. 2768