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. Naïma Saisissez du texte, l'adresse d'un site Web ou importez un document à traduire. <http: translate.google.fr="" ?tr="f&amp;hl=fr"> Annuler <http: translate.google.fr="" ?tr="t&amp;hl=fr"> [[alternative HTML version deleted]]

Naima, Why do you need to filter genes? For bad quality or some other reasons in your mind? Read my recent paper you may have an idea: http://www.ncbi.nlm.nih.gov/pubmed/20846437 Wayne -- 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&amp;hl=fr"> > Annuler <http: translate.google.fr="" ?tr="t&amp;hl=fr"> > > > [[alternative HTML version deleted]] > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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

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&amp;hl=fr"> > Annuler <http: translate.google.fr="" ?tr="t&amp;hl=fr"> >