[BioC] Disorderly duplicate spots

[Yannick Wurm]

Hi Naomi & Jim,

thanks for your replies!
I'll look into doing something along the same lines as you did Naomi.

Have a wonderful weekend,

Yannick

On Jan 17, 2008, at 16:00 , Naomi Altman wrote:

> 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
>>