I am used to seeing 2 modes, although the second mode has been further to the left on the (older, whole genome) chips I have seen. --Naomi At 02:05 PM 11/28/2011, James W. MacDonald wrote: >Hi Assa, > > >On 11/28/2011 7:48 AM, Assa Yeroslaviz wrote: >>Hello BioC Users, >> >>I have a problem interpreting my data. >>I am analyzing my microarray data and did a density plot of my pm values >>for the six arrays. >> >>I am getting a strange behavior of these arrays. Instead of getting one >>peak for the data as it is usually is ( at least as fat as I know it), I am >>getting two peaks (see the image attached). >>The good news is that they all behave similarly, so it might be normal, but >>I just don't get it. > >It depends on the chip, IME. The Gene ST and Exon chips tend to have >this distribution, whereas the older 3'-biased chips seemed to me to >be more unimodal. > >Best, > >Jim > > >> >>I would appreciate any ideas as to the rasons behind this behavior. >> >>Thanks >>A. >> >> >>_______________________________________________ >>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 > >-- >James W. MacDonald, M.S. >Biostatistician >Douglas Lab >University of Michigan >Department of Human Genetics >5912 Buhl >1241 E. Catherine St. >Ann Arbor MI 48109-5618 >734-615-7826 > >********************************************************** >Electronic Mail is not secure, may not be read every day, and should >not be used for urgent or sensitive issues >_______________________________________________ >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