Hi! I have a problem concerning the Limma package, version 1.3.1 and 1.3.2. I normally run: RG.median.no.back.w01 <- read.maimages(files,"genepix",columns=list(Rf="F635.Median",Gf="F532.M edian",Rb="F3.SD",Gb="F3.SD"),wt.fun=wtflags(0.1)) The Rb=F3.SD and Gb=F3.SD are just columns with 0 zeros in. However in the new packages for the help file for ma.images it says: # Read all .gpr files from current working directory # and give weight 0.1 to spots with negative flags ## Don't run: files <- dir(pattern="*\\.gpr$") RG <- read.maimages(files,"genepix",wt.fun=wtflags(0.1)) ## End Don't run # Read all .spot files from current working director and down-weight # spots smaller or larger than 150 pixels ## Don't run: files <- dir(pattern="*\\.spot$") RG <- read.maimages(files,"spot",wt.fun=wtarea(150)) ## End Don't run Do you know what the problem is, and how do I read in my data now? Sincerely, Kim Kultima ------------------------------------------------------------------- Kim Kultima Department of Pharmaceutical Biosciences Division of Toxicology Uppsala University The Biomedical Center Box 594 SE-75124 Uppsala Sweden Phone +46-18-4714254 Fax +46-18-4714253 Email: Kim.Kultima@farmbio.uu.se Home Page http://www.farmbio.uu.se/tox/index.html ------------------------------------------------------------------- [[alternative HTML version deleted]]

Dear Kim, Nothing has changed regarding read.maimages() in the new versions of limma. All the lines saying "##Don't run:" are (very confusing) messages written by R 1.8.0 not by the package author! Just ignore them. (The reason for the "Don't run" messsages is to indicate that these lines will not normally execute for you unless you have suitable data files in your working directory, i.e., the message means don't run these commands as they are!) Gordon At 11:41 PM 11/11/2003, Kim Kulltima wrote: >Hi! > >I have a problem concerning the Limma package, version 1.3.1 and 1.3.2. >I normally run: >RG.median.no.back.w01 <- >read.maimages(files,"genepix",columns=list(Rf="F635.Median",Gf="F532. Median",Rb="F3.SD",Gb="F3.SD"),wt.fun=wtflags(0.1)) > >The Rb=F3.SD and Gb=F3.SD are just columns with 0 zeros in. > >However in the new packages for the help file for ma.images it says: > ># Read all .gpr files from current working directory ># and give weight 0.1 to spots with negative flags > >## Don't run: >files <- dir(pattern="*\\.gpr$") >RG <- read.maimages(files,"genepix",wt.fun=wtflags(0.1)) >## End Don't run > ># Read all .spot files from current working director and down-weight ># spots smaller or larger than 150 pixels > >## Don't run: >files <- dir(pattern="*\\.spot$") >RG <- read.maimages(files,"spot",wt.fun=wtarea(150)) >## End Don't run > > >Do you know what the problem is, and how do I read in my data now? > >Sincerely, > >Kim Kultima