[BioC] Disorderly duplicate spots

[Naomi Altman]

Dear Yannick,
On the whole, most people have equal numbers of duplicates for each 
gene, and can use the methods discussed in limma.

However, we had a situation similar to yours.

First, we did a graphical analysis to determine if the expression 
profile of a clone set was fairly parallel over the arrays.  A 
parallel profile indicates that the assessment of differential 
expression will be the same for any clone.  (Almost all of ours were, 
and we suspect that some of the others were possibly assembly 
errors.)  Then we picked the clone that was at a reasonably high 
quantile of the expression distribution.  i.e. we did not pick the 
most highly expressed clone, in case this was due to some type of 
error.  We picked the median, or the clone at the 75th percentile etc.

--Naomi

At 07:48 AM 1/17/2008, Yannick Wurm wrote:
>Dear List,
>
>I am a graduate student working with the fire ant Solenopsis invicta.
>We did some two-color cDNA microarrays that I've begun analyzing with
>limma. But something feels wrong about how I'm doing things: we
>printed whole clones from a ~25,000 clone cDNA library onto our
>microarray. Simultaneously, we sequenced our clones. They assemble to
>~12,000 transcripts. Many are singlets, but some transcripts are
>represented by multiple clones (one transcript is represented by 32
>clones!).
>
>So during analysis, treating each clone as independent feels wrong.
>It means:
>         - correcting for 25,000 multiple tests rather than 10,000, thus
>reducing my power;
>         - and not taking into account the technical replication we get by
>multiple spots on the array.
>
>The limma manual has a section on Within-Array Replicate Spots. But
>only mentions what to do for people who have a single duplicate of
>every spot on their array.
>
>I'm sure other people have had to deal with this in the past. Do you
>have any pointers?
>
>Thanks & regards,
>
>Yannick
>
>
>--------------------------------------------
>           yannick . wurm @ unil . ch
>Ant Genomics, Ecology & Evolution @ Lausanne
>    http://www.unil.ch/dee/page28685_fr.html
>
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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