Hi Alicia, I checked the length annotation, it was fine. Also I looked at the pwf plot for counts bias, it looks even flatter (no bias). But I was wondering why there are only a few points on the plot, if we looking at gene length vs proportion of DE genes? As I mentioned in the previous email, I have 1802 DE genes and 28771 nonDE genes in my samples. Here is the plot for the count bias. https://docs.google.com/open?id=0B_mk9qnFziV- aEhjeGZsY3BSVC1tMWUwTElzWENXQQ Thanks, Al On Sun, Feb 26, 2012 at 4:49 PM, Alicia Oshlack <alicia.oshlack@mcri.edu.au>wrote: > Hi Al, > > To me the plot looks like a perfectly good fit to the data. The thing is > that it doesn't look like there is much gene length bias in the plot that > you have shown. I'm not really sure why this would be as it is usually a > strong effect but perhaps the biological signal is even stronger than this > technical effect? You might just want to check the matching of your gene > length annotation to DE genes, just in case. > > Cheers, > Alicia > > > From: Alpesh Querer <alpeshq@gmail.com> > > To: bioconductor@r-project.org > > Subject: [BioC] Goseq plot > > Message-ID: > > <cao0xdqpci- dntu+yckafuf6h5wdjofj954ot+ktrto_ngu="xFA@mail.gmail.com"> > > Content-Type: text/plain > > > > Hi Goseq ers, > > > > I followed the user manual for Goseq and came up with the following > plot, I > > am working with corn data, so > > I imported the lengths from Biomart and manually created the annotation. > > Can you please guide me if the Pwf plot is a good fit for my data, > > also is there a way to find which of gene-length and counts to use as > > bias.data. The plot is for gene length bias. > > I have 1802 DE genes and 28771 nonDE genes in my samples (edgeR output) . > > Also if the plotPWF function plots > > the pwf values, why only a handful of values can be seen in this plot? > > Please pardon my statistical ignorance. > > > > > https://docs.google.com/open?id=0B_mk9qnFziV- SHE0LXQ0ZUFUb0dNMEEzN1UwVGhjQQ > > > > Many Thanks, > > Al > > > > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]