Hi, I'm learning using marray package to analyze microarray data. After studying the tutorial using data 'swirl', I found each spot in this tutorial slide stands for one gene. My data have a little difference. These are 3 replicated spots in each slide. I didn't find the comand dealing with replicated spots when I followed the tutorial, So, when I analyzed 4 replicated slides and output the gene list using command sunch as "stat.bayesian" function, each gene ID in the list stands for only one spot in the slides instead of 3 replicated spots. I want each gene stands for all spot data including 3 replicated spots in each slide. Can sombody give me some hints to deal with this case? If I need to set up some arguments in marrayLayout or I have to write some function? My data is GenePix fata, My Gal file like this: ATF 1 43 5 Type=GenePix ArrayList V1.0 BlockCount=40 BlockType = 0 "Block1= 2600 17000 140 16 250 18 250" ......... "Block40= 16100 57500 140 16 250 18 250" Block Row Column ID Name 1 1 1 QHA10A21.yg.ab1 sf_1_1 1 1 2 QHA10A21.yg.ab1 sf_1_1 1 1 3 QHA10A21.yg.ab1 sf_1_1 1 1 4 QHA10P20.yg.ab1 sf_1_3 1 1 5 QHA10P20.yg.ab1 sf_1_3 1 1 6 QHA10P20.yg.ab1 sf_1_3 1 1 7 QHA11H15.yg.ab1 sf_1_5 1 1 8 QHA11H15.yg.ab1 sf_1_5 1 1 9 QHA11H15.yg.ab1 sf_1_5 1 1 10 QHA11O07.yg.ab1 sf_1_7 1 1 11 QHA11O07.yg.ab1 sf_1_7 1 1 12 QHA11O07.yg.ab1 sf_1_7 ........... Thanks Yi

The limma package has integrated support for replicated spots. In the terminology of that package you have ndups=3 and spacing=1. See lmFit() and eBayes(). > Hi, > > I'm learning using marray package to analyze microarray data. After > studying the tutorial using data 'swirl', I found each spot in this > tutorial slide stands for one gene. My data have a little difference. > These are 3 replicated spots in each slide. I didn't find the comand > dealing with replicated spots when I followed the tutorial, So, when I > analyzed 4 replicated slides and output the gene list using command > sunch as "stat.bayesian" function, stat.bayesian is not actually a bioconductor function but rather a function from the older SMA package. It's been superceded by the ebayes function in limma. You may need to upgrade your packages. Gordon each gene ID in the list stands for > only one spot in the slides instead of 3 replicated spots. I want each > gene stands for all spot data including 3 replicated spots in each > slide. Can sombody give me some hints to deal with this case? If I need > to set up some arguments in marrayLayout or I have to write some > function? > > My data is GenePix fata, My Gal file like this: > > ATF 1 > 43 5 > Type=GenePix ArrayList V1.0 > BlockCount=40 > BlockType = 0 > "Block1= 2600 17000 140 16 250 18 250" > ......... > "Block40= 16100 57500 140 16 250 18 250" > > Block Row Column ID Name > 1 1 1 QHA10A21.yg.ab1 sf_1_1 > 1 1 2 QHA10A21.yg.ab1 sf_1_1 > 1 1 3 QHA10A21.yg.ab1 sf_1_1 > 1 1 4 QHA10P20.yg.ab1 sf_1_3 > 1 1 5 QHA10P20.yg.ab1 sf_1_3 > 1 1 6 QHA10P20.yg.ab1 sf_1_3 > 1 1 7 QHA11H15.yg.ab1 sf_1_5 > 1 1 8 QHA11H15.yg.ab1 sf_1_5 > 1 1 9 QHA11H15.yg.ab1 sf_1_5 > 1 1 10 QHA11O07.yg.ab1 sf_1_7 > 1 1 11 QHA11O07.yg.ab1 sf_1_7 > 1 1 12 QHA11O07.yg.ab1 sf_1_7 > ........... > > Thanks > > Yi > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor