[BioC] Patricia's simpleaffy question

Fri Jan 18 14:35:45 CET 2008

Ok Alex

I didn´t pay attention... sorry

Thanks for your help!

Patricia

>  Dear Patricia,
> Please do not hijack a thread and ask a different question to the subject
> line.
>
> How many genes depends on your arrays quality and the biology of your
> experiment. There will be some genes that are silent across all of the
> conditions. Why don't you plot the mean expression and variance of all
> probesets to see what those distributions look like?
>
> RMA is generally regarded as better than MAS5.
>
> Cheers,
> Alex
>
> --------------------------------------------
> Alex C. Lam
> Roslin Institute (Edinburgh)
> Midlothian
> EH25 9PS
> United Kingdom
> Tel: +44 131 5274471
>
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>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Patrícia
> Luiza Nunes da Costa
> Sent: 18 January 2008 12:50
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Disorderly duplicate spots
>
> Friends,
>
> We used an Affymetrix microarray with about 45 000 genes. We have 4 groups
> with 3 arrays.
> How many genes should I except after par wise filtering (simpleaffy)?  I
> know it depends on the parameters and stringency, but I want to know an
> average, or the minimum, to perform a statistical analysis.
> What algorithm do you think its better: RMA or MAS 5?
>
> Thanks and regards,
>
> Patrícia
>
>
>
>
>
>
>> 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
>>>>
>>
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>
>
> Patrícia Luiza Nunes da Costa
> Laboratório de Oncologia Experimental, Grupo de Adesão Celular Faculdade
> de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112
> Cerqueira Cesar Cep 01246-903
> Tel: (11) 3061-7486 e (11) 8202-7073
>
>
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Patrícia Luiza Nunes da Costa
Laboratório de Oncologia Experimental, Grupo de Adesão Celular
Faculdade de Medicina da Universidade de Paulo-FM USP
Av. Dr. Arnaldo, 455 sala 4112
Cerqueira Cesar
Cep 01246-903
Tel: (11) 3061-7486 e (11) 8202-7073

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Esta mensagem foi verificada
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