[BioC] Limma and Dye Flips

[Jianping Jin]

A related question:

Does limma algorithms for dye swap use "weights" for dye flip arrays if not 
every sample had dye swap replication?  For example there are 3 normal vs. 
tumor arrays, but only one array with different dye-orientation.

thanks,

JJ

--On Thursday, January 24, 2008 4:08 PM +0000 Claus-Dieter Mayer 
<claus at bioss.ac.uk> wrote:

> Hi Sally,
>
> What you have done (averaging across the dye-flips) is basically ok, as
> the information you loose by doing that only concerns technical
> variability. The more sophisticated way of doing things would be to
> include all arrays, but to change your limma analysis by
> a) adding a dye effect (cf. limma tutorial)
> b) adding a block effect that informs the analysis about which arrays
> are technical replicates (dye-flips), that analyse the same biological
> samples (again see the limma tutorial for details).
>
> In addition to your treatment effect this analysis will give you
> information about gene-specific dye-effects and the correlation between
> the two dye-flips. Both of these might not be relevant to the biological
> question of interest, but be helpful from a quality control perspective.
> If you average the dye-flips you eliminate  the gene-specific dye-effect
> (which is good), but you also loose the information about it. Equally
> you give up the information about the technical array to array (+dye
> flip)-variation. The fold-changes you estimate for your biological
> effect of interest will be identical for both approaches but p-values
> etc will differ slightly. From the point of statistical power both
> approaches should be similar as far as I can see (and others may correct
> me if I overlooked any subtle points here).
>
> Best Wishes
>
> Claus
>
>
>
> Sally wrote:
>> My question is about handling dye flips in Limma.
>>
>> In my experiment I did a dye flip for each comparison.  When I finished
>> the preprocessing I averaged the M values of the two dye flip arrays.Now
>> I am fitting a linear model.  Should I have averaged the dye flips
>> before, or should the dye flips be incorporated in the linear model?
>>
>> Sally Goldes
>> 	[[alternative HTML version deleted]]
>>
>> _______________________________________________
>> 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
>>
>>
>>
>>
>>
>>
>> Click link below to report this email as spam.
>> https://www.mailcontrol.com/sr/ubMazK5f8H7cohtw78djyfAVCukN02RG8MraHiLp2
>> brog64sJZMbax70VQcaVVh5T7KYBPDklBRfAchUXJwv+Q==
>>
>>
>>
>
> --
> *************************************************************************
> **********  Dr Claus-D. Mayer                    | http://www.bioss.ac.uk
>  Biomathematics & Statistics Scotland | email: claus at bioss.ac.uk
>  Rowett Research Institute            | Telephone: +44 (0) 1224 716652
>  Aberdeen AB21 9SB, Scotland, UK.     | Fax: +44 (0) 1224 715349
>
> _______________________________________________
> 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



##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu