Does anyone try ACME on medip-chip? On Wed, Jun 15, 2011 at 12:38 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Tue, Jun 14, 2011 at 9:07 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Tue, Jun 14, 2011 at 6:34 PM, Adeolu Adewoye <badicrown at="" hotmail.com=""> wrote: >>> >>> Dear Sean, >>> >>> I am trying to analyse my NimbleGen MeDIP-chip data using your ACME package >>> but have few questions. >>> >>> The output file from findRegions command generate suggested enrichment >>> regions based on the chosen threshold right? What is the statistical test >>> involved ( in order word the output suggested enrichment showing mean and >>> median? Is it possible to also output the pValue or probability of >>> enrichment? >> >> The ?findRegions function simply uses a threshold (default 1e-4) >> p-values from a moving-window chi-square test at each probe. ?All of >> the regions reported by findRegions that have a value of TRUE in the >> TF (for True/False) column are considered "positive" and you will need >> to play with the findRegions threshold a bit to find what works "best" >> for your experiment. ?The mean and median values that are output by >> findRegions can be used in a ranking fashion with higher means or >> medians being "more enriched". >> >>> >>> Can you also please explain a bit more on how to load and view .sgr file in >>> the UCSC Genome Browser? >> >> .sgr files are meant to be loaded into the IGB browser. ?I do not >> think the .sgr file format is supported by the UCSC genome browser. > > Hi, Adeolu. > > I added a simple write.bedGraph() function to ACME to generate > bedGraph format files for UCSC. ?It is available in the devel branch > (in a day or so), version 2.9.1 of ACME. > > Sean > > >>> >>> Please not that?I have tried few things to ask for help using the >>> bioconductor distribution list with no response. >> >> Sorry about that. ?Thanks for being persistent. >> >> Sean >> > > _______________________________________________ > 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

Does anyone try ACME on medip-chip? On Wed, Jun 15, 2011 at 12:38 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Tue, Jun 14, 2011 at 9:07 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Tue, Jun 14, 2011 at 6:34 PM, Adeolu Adewoye <badicrown at="" hotmail.com=""> wrote: >>> >>> Dear Sean, >>> >>> I am trying to analyse my NimbleGen MeDIP-chip data using your ACME package >>> but have few questions. >>> >>> The output file from findRegions command generate suggested enrichment >>> regions based on the chosen threshold right? What is the statistical test >>> involved ( in order word the output suggested enrichment showing mean and >>> median? Is it possible to also output the pValue or probability of >>> enrichment? >> >> The ?findRegions function simply uses a threshold (default 1e-4) >> p-values from a moving-window chi-square test at each probe. ?All of >> the regions reported by findRegions that have a value of TRUE in the >> TF (for True/False) column are considered "positive" and you will need >> to play with the findRegions threshold a bit to find what works "best" >> for your experiment. ?The mean and median values that are output by >> findRegions can be used in a ranking fashion with higher means or >> medians being "more enriched". >> >>> >>> Can you also please explain a bit more on how to load and view .sgr file in >>> the UCSC Genome Browser? >> >> .sgr files are meant to be loaded into the IGB browser. ?I do not >> think the .sgr file format is supported by the UCSC genome browser. > > Hi, Adeolu. > > I added a simple write.bedGraph() function to ACME to generate > bedGraph format files for UCSC. ?It is available in the devel branch > (in a day or so), version 2.9.1 of ACME. > > Sean > > >>> >>> Please not that?I have tried few things to ask for help using the >>> bioconductor distribution list with no response. >> >> Sorry about that. ?Thanks for being persistent. >> >> Sean >> > > _______________________________________________ > 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