[BioC] averaging replicates within arrays

[alex lam (RI)]

Dear Gordon,
Thanks for your reply. The probes are identical and every gene is replicated but not in the same number. Some are replicated 3 times and some 6 times. Is that going to be a problem?

I should rephrase the comment on the spots with zero weights. I knew that they were ignored in normalization. Are they also ignored in other limma methods? I had to explicitly exclude them in boxplot, but I guess boxplot is just a generic method.

Regards,
Alex
------------------------------------
Alex Lam
PhD student
Department of Genetics and Genomics
Roslin Institute (Edinburgh)
Roslin
Midlothian EH25 9PS

Phone +44 131 5274471
Web   http://www.roslin.ac.uk


-----Original Message-----
From: Gordon Smyth [mailto:smyth at wehi.edu.au]
Sent: 08 November 2005 23:17
To: alex lam (RI)
Cc: BioC Mailing List
Subject: [BioC] averaging replicates within arrays


Dear Alex,

Do you have the same number of replicate spots for every gene of interest 
and are the replicate probes identical? If so, see the case study in limma 
User's Guide on "Within array replicate spots".

If only some of your genes are replicated, or if the probes are not 
identical, I would strongly advice you not to attempt to pre-emptively 
average the spots. There is little to be gained and much to be lost.

I don't understand you comment about ignoring spots with zero weight. limma 
already does this.

Best wishes
Gordon

>[BioC] averaging replicates within arrays
>alex lam (RI) alex.lam at bbsrc.ac.uk
>Tue Nov 8 23:49:46 CET 2005
>
>Dear Colleagues,
>
>Hi, I am a first year PhD student recently started on a project involving 
>microarray data analysis at the Roslin Institute in Scotland. I have 
>managed to follow the limma  vignette in loading the data and performed 
>the default normalization within arrays. On each array, probes of the same 
>genes have been placed in more than one spot. What I would like is to do 
>is to group spots by gene names in MA$genes and calculate the average 
>logratio as the expression level (better still, ignore the spots with zero 
>weight).
>
>I guess I can dump the data and process it in perl but would like to know 
>how to do this a bit more elegantly in R. Your help is greatly appreciated.
>
>Many thanks,
>Alex