Hello, I am using marrayInput packages to do my data analysis. After I read into my data with read.marrayRaw function. I found that lots of my data is labelled "NA". I use name.Gf="Ch1 Median",name.Rf="Ch2 Median",name.Gb=" Ch1 B Median",name.Rb="Ch2 B Median" command, I am wondering how marrayClass transformed data. Is still M vs A or what. I want to normalize my data with this packages, then export to do further analysis with other software. Any explanation is greatly appreciated about this algorithm Thanks

Hi Joyce, Usually, NA's comes from higher background the foreground values. One way is not to do local background subtraction before performing normalization. e.g. say dataraw is a marrayRaw object dataraw@maGb <- dataraw@maRb <- matrix(0,0,0) datanorm <- maNorm(dataraw) write.xls(datanorm@maM, file="Norm.xls") Cheers Jean On Wed, 18 Feb 2004, Joyce Gu wrote: > Hello, > I am using marrayInput packages to do my data analysis. After I read into my > data with read.marrayRaw function. I found that lots of my data is labelled > "NA". I use name.Gf="Ch1 Median",name.Rf="Ch2 Median",name.Gb=" Ch1 B > Median",name.Rb="Ch2 B Median" command, I am wondering how marrayClass > transformed data. Is still M vs A or what. > I want to normalize my data with this packages, then export to do further > analysis with other software. > > Any explanation is greatly appreciated about this algorithm > > Thanks > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Dear Ms. Gu: The following message appears to be in reference to a problem similar to the one you're having. http://www.mail-archive.com/r-help@stat.math.ethz.ch/msg13521.html Note that the author of that message seems to be running an older version of R. If that's not your problem, then doing the thing he tried might work for you-- namely invoking R with the --max-mem-size=1024M command-line flag. Alternatively, you can set the memory limit from inside of R with this command: memory.limit(size=1024) By the way, how much RAM do you have in your computer and how large is the swap-file? >Hi, >I am using marrayClasses package to read my raw data into R. >I have 89 arrays, I put them in the same directory, and read them all. but I got the following error messages, >Error: cannot allocate vector of size 3828 Kb >What is the maximum size marray package can handle to read into R? > > > I suspect this error message indicates that R is incorrectly parsing the number of rows and columns. How many rows and columns does it report reading? Do they match what's supposed to be in your data? I don't know about this particular package, but when I have this problem reading tabular data in general, changing the column names and row names so they contain no spaces usually fixes it. >Also,I tried to read one file at a time, I got the following messages, >Warning messages: >1: number of items read is not a multiple of the number of columns >2: NAs introduced by coercion >3: NAs introduced by coercion >4: NAs introduced by coercion >5: NAs introduced by coercion > -- --Sincerely, Alex F. Bokov Department of Physiology UTHSCSA ------------------------------------------------------------ "Dealing with failure is easy: Work hard to improve. Success is also easy to handle: You've solved the wrong problem. Work hard to improve." - Alan Perlis