Hi, I have a question regarding the NGS (RNA-Seq) analysis. We have a time course data regarding embryo development: 8 time points from different day mouse embryos and did RNA-seq on these samples. But we have only one sample for each time point. I knew that there are some bioc packages for NGS analysis (edgeR, DESeq, etc). Is any package or method good for one-sample-per-time-point data? Thank you. Xing [[alternative HTML version deleted]]

Dear Xing, Last time I looked, edgeR, DESeq, etc were meant to test differences in means, which requires replication. For a time course without replication, you probably need a regression-type analysis - e.g. fitting a negative-binomial regression on time for each gene. Then the deviations from the model are used to assess the statistical significance of the pattern. To do this, you need an a priori idea of the pattern - e.g. cosine waves for periodic genes and polynomials for linear or slightly curved genes. An ad hoc method would be to do some expression clustering based on e.g. Spearman correlation to cluster the genes into 3 or 4 clusters with roughly similar shapes. Then do regression on an appropriate basis in each cluster, using a generalized linear model. --naomi At 02:23 PM 3/2/2011, Xing Li wrote: >Hi, > >I have a question regarding the NGS (RNA-Seq) analysis. > >We have a time course data regarding embryo development: 8 time points from >different day mouse embryos and did RNA-seq on these samples. But we have >only one sample for each time point. > >I knew that there are some bioc packages for NGS analysis (edgeR, DESeq, >etc). Is any package or method good for one-sample-per-time-point data? > >Thank you. > >Xing > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Xing What hypothesis do you want to test? Are you looking to detect genes changing over time, or something more complicated? To give some more advice about how to approach your analysis using tools such as edgeR it would help to know more about what you are hoping to learn from your experiment. Cheers Davis On Mar 3, 2011, at 6:23 AM, Xing Li wrote: > Hi, > > I have a question regarding the NGS (RNA-Seq) analysis. > > We have a time course data regarding embryo development: 8 time points from > different day mouse embryos and did RNA-seq on these samples. But we have > only one sample for each time point. > > I knew that there are some bioc packages for NGS analysis (edgeR, DESeq, > etc). Is any package or method good for one-sample-per-time-point data? > > Thank you. > > Xing > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ---------------------------------------------------------------------- -- Davis J McCarthy Research Technician Bioinformatics Division Walter and Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville, Vic 3052, Australia dmccarthy at wehi.edu.au http://www.wehi.edu.au ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}