Dear List Members, First - my experiment I have 7 time points and two treatments (cold and control). I used two-colour microarrays, each RNA was hybridized with a common reference (time zero). I've searched list's archive and read the tutorial but still I can't figure out how can I analyze this experiment (two-colour with common reference) in maSigPro. I know that I have to split my data (long time series). I'd like to make two variants of analysis: 1 - Normalization in limma, analysis in maSigPro. 2 - ASCA-genes, then analysis in maSigPro (normalization?). My questions are: (1) - Should I use log-ratio (time_point to time_zero on each microarray) in analysis? (2) - How experimental design file should look like in this case? I've read about ASCA-genes methodology, which can be used as a preprocessing method to subsequent analysis in maSigPro. I've found codes but I don't know how the results from ASCA-genes can be passed to maSigPro. Should I normalize the data before using ASCA-genes? Help will be very appreciated. Best Regards, Maciej Jo?czyk, MSc Department of Plant Molecular Ecophysiology Institute of Plant Experimental Biology Faculty of Biology, University of Warsaw 02-096 Warszawa, Miecznikowa 1 ___________________________________ NOCC, http://nocc.sourceforge.net -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com

Dear Maciej, You can apply maSigPro with 7 time-points without splitting the data. The method is going to work well. You must split the data if the obtained models don't fit very well. Splitting the data is not implemented automatically in the maSigPro R-program and you have to elaborate a more complicate design. We have developed a web-service where we have implemented maSigPro and other tools http://sea.bioinfo.cipf.es/. We have tried to simplify things. If you want apply maSigPro easily you can use it. We are checking that all work well. If you use it you could send your opinion. You can visit the "help" to see examples: data and results. Regarding your question, it is not necesary to use log-ratio (time_point to time_zero on each microarray) to apply maSigPro. On the other hand ASCA-genes is also a methodology to detect significant genes. We are developing an strategy based on ASCA to eliminate the bacth effect. This is a preprocessing technique but it is not a normalization method. We haven't published anything about this yet. Where did you hear about it?When we finish all the things we will add in SEA web-service also this tool. Best wishes, Mar?a. ----- Original Message ----- From: "Maciej Jo?czyk" <mjonczyk@biol.uw.edu.pl> To: <bioconductor at="" stat.math.ethz.ch=""> Cc: "Maciej Jo?czyk" <mjonczyk at="" biol.uw.edu.pl=""> Sent: Tuesday, April 20, 2010 1:48 PM Subject: [BioC] [maSigPro] How to analyze 2-colour microarrays? > Dear List Members, > > First - my experiment > > I have 7 time points and two treatments (cold and control). > I used two-colour microarrays, each RNA was hybridized with a common > reference (time zero). > > I've searched list's archive and read the tutorial but still I can't > figure out how can I analyze this experiment (two-colour with common > reference) in maSigPro. > I know that I have to split my data (long time series). > > I'd like to make two variants of analysis: > > 1 - Normalization in limma, analysis in maSigPro. > > 2 - ASCA-genes, then analysis in maSigPro (normalization?). > > My questions are: > > (1) - Should I use log-ratio (time_point to time_zero on each > microarray) in analysis? > (2) - How experimental design file should look like in this case? > > I've read about ASCA-genes methodology, which can be used as a > preprocessing method to subsequent analysis in maSigPro. I've found > codes but I don't know how the results from ASCA-genes can be passed to > maSigPro. > > Should I normalize the data before using ASCA-genes? > > Help will be very appreciated. > Best Regards, > > Maciej Jo?czyk, MSc > Department of Plant Molecular Ecophysiology > Institute of Plant Experimental Biology > Faculty of Biology, University of Warsaw > 02-096 Warszawa, Miecznikowa 1 > > > > ___________________________________ > NOCC, http://nocc.sourceforge.net > > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com > > _______________________________________________ > 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