Fanny, Thanks for the feedback! Yes, it is a mistake. If you use the default setting of peaksNearBDP, then it will not affect the results. I will update the dev version and keep you updated. Best regards, Julie On 8/7/12 10:51 AM, "EYBOULET Fanny 228361" <fanny.eyboulet@cea.fr> wrote: Hello, I’m using ChIPpeakAnno 2.4.0 to annotate my peaks after peakcalling with Bayespeak. There is no problem when I use the command annotatePeakInBatch but I have a question about the command peaksNearBDP. When I looked a little closer to the script, I noticed that the peaklocfordistance is not calculated the same way for plus and minus annotations. Here are the lines I’m talking about : plus = annotatePeakInBatch(myPeakList, AnnotationData = AnnoPlus, PeakLocForDistance = PeakLocForDistance, FeatureLocForDistance = FeatureLocForDistance) minus = annotatePeakInBatch(myPeakList, AnnotationData = AnnoMinus) Is there an explanation for this difference ? Or is it a mistake? Thanks in advance for your answer. Sincerely. Fanny Eyboulet PhD student DSV/iBiTec-s/SBIGeM/LREGE Bat. 144 CEA Saclay 91191 Gif sur Yvette Cedex France Tel : 0169086125 @ : fanny.eyboulet@cea.fr [[alternative HTML version deleted]]

Fanny, The bug has been fixed. Please download ChIPpeakAnno 2.5.11 if you need to set PeakLocForDistance and/or FeatureLocForDistance in peaksNearBDP. Thanks again for your feedback! Best regards, Julie On 8/7/12 11:25 AM, "Lihua Julie Zhu" <julie.zhu at="" umassmed.edu=""> wrote: > Fanny, > > Thanks for the feedback! Yes, it is a mistake. If you use the default setting > of peaksNearBDP, then it will not affect the results. I will update the dev > version and keep you updated. > > Best regards, > > Julie > > > On 8/7/12 10:51 AM, "EYBOULET Fanny 228361" <fanny.eyboulet at="" cea.fr=""> wrote: > > Hello, > I?m using ChIPpeakAnno 2.4.0 to annotate my peaks after peakcalling with > Bayespeak. > There is no problem when I use the command annotatePeakInBatch but I have a > question about the command peaksNearBDP. When I looked a little closer to the > script, I noticed that the peaklocfordistance is not calculated the same way > for plus and minus annotations. Here are the lines I?m talking about : > plus = annotatePeakInBatch(myPeakList, AnnotationData = AnnoPlus, > PeakLocForDistance = PeakLocForDistance, FeatureLocForDistance = > FeatureLocForDistance) > minus = annotatePeakInBatch(myPeakList, AnnotationData = AnnoMinus) > Is there an explanation for this difference ? Or is it a mistake? > Thanks in advance for your answer. > Sincerely. > > > > Fanny Eyboulet > PhD student > DSV/iBiTec-s/SBIGeM/LREGE > Bat. 144 CEA Saclay > 91191 Gif sur Yvette Cedex France > Tel : 0169086125 > @ : fanny.eyboulet at cea.fr > > > > [[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