Dear All, Why is the volcano plot from limma package is more beautiful ( symmetrical ) than that from raw t.test calculation? Please see attachment for the picture. Best regards, Allen 2014-08-18 my1stbox -------------- next part -------------- A non-text attachment was scrubbed... Name: pic.png Type: image/png Size: 354776 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140818="" 262fc00e="" attachment.png="">

Hi, Allen. It looks like the scatter plot shows different data for the t-test and for the limma results. Perhaps one dataset was normalized and the other was not or two different normalizations or filters were used? Sean On Sun, Aug 17, 2014 at 9:16 PM, my1stbox <my1stbox at="" 163.com=""> wrote: > Dear All, > Why is the volcano plot from limma package is more beautiful ( symmetrical > ) than that from raw t.test calculation? Please see attachment for the > picture. > > Best regards, > Allen > > 2014-08-18 > > > my1stbox > _______________________________________________ > 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 > [[alternative HTML version deleted]]