Hi all, I am trying to find out more about the use of flags by the marray package. In particular for normalization purposes. It seems that if I read a set of array files with flags and perform, say, loess print tip normalization and then I replace all flags with zeroes and repeat the analysis, I am not getting the same results.... sometimes quite different. Note that I have a whole zoo of flags in these data: a good share of -50, -75 and -100... a lot of them introduced manually by a human operator to mark "visually suspicious" array sectors. Is there any document that explains the internal use of flags by the normalization functions in marray? Thanks in advance! Juan Pedro -- ============================= Juan Pedro Steibel Postdoctoral researcher Statistical Genetics Department of Animal Science Michigan State University 1205-I Anthony Hall East Lansing, MI 48823 USA Phone: 1-517-353-5102 E-mail: steibelj at msu.edu

Hello again, I already figured out a problem in my script and realized that (by default) the flags are being ignored by the normalization routines. Please, disregard my previous email. Thanks JP Juan Pedro Steibel wrote: > Hi all, > > I am trying to find out more about the use of flags by the marray > package. In particular for normalization purposes. > > It seems that if I read a set of array files with flags and perform, > say, loess print tip normalization and then I replace all flags with > zeroes and repeat the analysis, I am not getting the same results.... > sometimes quite different. > > Note that I have a whole zoo of flags in these data: a good share of > -50, -75 and -100... a lot of them introduced manually by a human > operator to mark "visually suspicious" array sectors. > > Is there any document that explains the internal use of flags by the > normalization functions in marray? > > Thanks in advance! > Juan Pedro > > -- ============================= Juan Pedro Steibel Postdoctoral researcher Statistical Genetics Department of Animal Science Michigan State University 1205-I Anthony Hall East Lansing, MI 48823 USA Phone: 1-517-353-5102 E-mail: steibelj at msu.edu