[BioC] Limma -time course - no replicates

Tan, Yifang Yifang.Tan at nrc-cnrc.gc.ca
Tue Jun 8 19:15:31 CEST 2010

Hi, Lana:

I have the similar question without biological replicates, and not yet confirmed. I am aware of my experiment was not well set-up strictly following to MIAME, which is quite common in plant research. 
This is my experiment is:
>>               FileName        DPA     Cy3     Cy5
>> 2009-07-10-atq3.7.3.145-15.gpr        15DPA   WT      MUTANT
>> 2009-07-15-atq3.7.3.146-15.gpr        15DPA   MUTANT  WT
>> 2009-07-15-atq3.7.3.147-15.gpr        15DPA   MUTANT  WT
>> 2009-07-15-atq3.7.3.148-15.gpr        15DPA   WT      MUTANT
>> 2009-07-15-atq3.7.3.149-15.gpr        15DPA   WT      MUTANT
>> 2009-07-17-atq3.7.3.151-20.gpr        20DPA   MUTANT  WT
>> 2009-07-17-atq3.7.3.152-20.gpr        20DPA   WT      MUTANT
>> 2009-07-17-atq3.7.3.153-25.gpr        25DPA   MUTANT  WT
>> 2009-07-17-atq3.7.3.154-25.gpr        25DPA   WT      MUTANT
>> 2009-07-17-atq3.7.3.155-10.gpr        10DPA   MUTANT  WT
>> 2009-07-17-atq3.7.3.156-10.gpr        10DPA   WT      MUTANT
>> 2009-07-17-atq3.7.3.157-30.gpr        30DPA   MUTANT  WT
>> 2009-07-17-atq3.7.3.158-30.gpr        30DPA   WT      MUTANT
>> 2009-07-21-atq3.7.3-159-10.gpr        10DPA   MUTANT  WT
>> 2009-07-21-atq3.7.3-160-20.gpr        20DPA   MUTANT  WT
>> 2009-07-21-atq3.7.3-164-25.gpr        25DPA   MUTANT  WT
>> 2009-07-21-atq3.7.3-256-30.gpr        30DPA   MUTANT  WT
>> 2009-07-22-atq3.7.3-115-10.gpr        10DPA   MUTANT  WT
>> 2009-07-22-atq3.7.3-116-20.gpr        20DPA   MUTANT  WT
>> 2009-07-22-atq3.7.3-117-25.gpr        25DPA   MUTANT  WT
>> 2009-07-22-atq3.7.3-118-30.gpr        30DPA   MUTANT  WT
>> 2009-07-22-atq3.7.3-119-10.gpr        10DPA   WT      MUTANT
>> 2009-07-22-atq3.7.3-120-20.gpr        20DPA   WT      MUTANT
>> 2009-07-22-atq3.7.3-124-25.gpr        25DPA   WT      MUTANT
>> 2009-07-22-atq3.7.3-125-30.gpr        30DPA   WT      MUTANT

Thanks any one, especially Naomi, who can give some suggestions.


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Lana Schaffer
Sent: Tuesday, June 08, 2010 10:29 AM
To: Naomi Altman; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Limma -time course - no replicates

Can you give an example how to set up the design matrix?

From: Naomi Altman [naomi at stat.psu.edu]
Sent: Tuesday, June 08, 2010 7:49 AM
To: Lana Schaffer; Naomi Altman; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Limma -time course - no replicates

You can use LIMMA.  The key is to have time be a continuous variable,
not a factor.  So time (or a function of time) is entered into the
design matrix, instead of +/- 1 or 0.


At 02:11 AM 6/6/2010, Lana Schaffer wrote:
>Can you please suggest a routine or software for us to use?
>From: Naomi Altman [naomi at stat.psu.edu]
>Sent: Friday, June 04, 2010 6:49 PM
>To: Lana Schaffer; bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Limma -time course - no replicates
>Only if you consider this to be a regression on a function of time,
>instead of an ANOVA.
>At 07:12 PM 6/4/2010, Lana Schaffer wrote:
> >Hi,
> >We are trying to use Limma code for a Time Course Experiment without
> >Replicates for 4 times.  From looking at the manual, looks like don't
> >Need replicates.  But the ebayes routine complains about no residual
> >Degrees of freedom.
> >Can we use Limma for Time Course without replicates?
> >Lana
> >
> >_______________________________________________
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>Naomi S. Altman                                814-865-3791 (voice)
>Associate Professor
>Dept. of Statistics                              814-863-7114 (fax)
>Penn State University                         814-865-1348 (Statistics)
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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