Entering edit mode
You might want to look at the 'genefilter' package which filters probe
sets based on different requirements, and there is a function to
filter out all control probe sets as well.
Also, given that there are over 50,000 probe sets on hgu133plus2
array, cut it down to 500-3000 for me sounds too harsh, although I
don't think there is a golden-standard about what would be a good
number after filtering. It depends on the design and expectations of
your experiment. However, for me ~26,000 probe sets afterwards have no
harm.
Cheers,
Yuan
On 29 Oct 2010, at 20:42, cstrato wrote:
> Dear Naima,
>
> Usually I prefer to reduce the number of probesets using "median
> absolute deviation" as prefilter (see e.g. ?madFilter). This reduces
> the number of probesets to about 500-3000 (depending on the cutoff).
> Afterwards I use either unitestFilter and fcFilter (see Chapter 5.2
> of xps.pdf), or I use the package "limma" which most people use (see
> Appendix A.3 how to create an ExpressionSet for use with limma).
> Generally I do not consider MAS5 detection calls to be sufficient
> for pre-filtering.
>
> I am sure that other people can give you a more detailed answer, but
> using "moderated t-statistics" is generally a good idea.
>
> Best regards
> Christian
>
>
> On 10/29/10 4:45 PM, Na?ma Oumouhou wrote:
>> Dear Christian,
>>
>> I'm sorry to bother you again : I've got a question about filter on
>> Affymetrix Human gene U133 Plus 2 array.
>> I would like to find differentiallty expressed genes between 2
>> groups of
>> patients (n1=7 and n2=6).
>> I have no experience in microarray analyses.
>> I read several publications and your xps vignettes but I don't know
>> what
>> I have to do.
>> Some people filtered probesets using Detection MAS5 call:probesets
>> that
>> aren't expressed in at least one sample using the Detection MAS5
>> algorithm are discarded.
>> What do you think about this filter?not tight enough?
>> After this filter and with my dataset,I still have 26 495
probesets?
>> Is
>> it too much?
>> Furthermore, in these remaining probesets, there are affymetrixx
>> control
>> probesets. These probesets have to be removed?At which step?
>> After, I use the moderated t-statistics with BH correction. I find
no
>> differentiallty expressed genes.
>> I wonder if I have to reduce the number of probesets with another
>> filter
>> or with a "Detection filter" tighter?
>> Thanks for any help.
>> Na?ma
>> Saisissez du texte, l'adresse d'un site Web ou importez un document
?
>> traduire. <http: translate.google.fr="" ?tr="f&hl=fr">
>> Annuler <http: translate.google.fr="" ?tr="t&hl=fr">
>>
>
> _______________________________________________
> 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
