Hello everyone, I tried to use limma package to read cDNA data into R, I tried the samples data swirl, it all works, but my cDNA data is not the same as the sample data, my data is tab-delimited .txt file, the header information is different from the sample provided, I am wondering is any way I can manupiated the function to be able to read customed data format with limma package, like pick up colume="string", just as read.marrayRaw()? Any idea is greatly appreciated! ******************************** Joyce Gu M.S. Scientific Programmer Cancer Genomics Group Baylor College of Medicine Phone: 832-824-4680 Fax: 832-825-4038

Hi Joyce, The function read.maimages() should be able to handle your custom format data. You can specify the columns you want to read in for the red foreground and background (Rf, Rb) and green foreground and background (Gf, Gb) using the 'columns' argument, which takes a list with components Rf="red foreground column name", Gf="green foreground column name", Rb="red background column name" and Gb="green background column name". For example, if I have 2 image analysis output files (array1.txt and array2.txt in tab delimited text format) in the current working directory, and I want the columns "F635 Mean" and "F532 Mean" for the red and green foregrounds and "B635 Median" and "B532 Median" for the red and green backgrounds, then the following commands: files <- dir(pattern=".txt") files # [1] "array1.txt" "array2.txt" RG <- read.maimages(files, columns=list(Rf="F635 Mean", Rb="B635 Median", Gf="F532 Mean", Gb="B532 Median")) will read in the relevant columns and store them in an RGList object. Alternatively, if your image analysis data is from one of the packages Spot, GenePix, SMD, Imagene, Arrayvision or Quantarray, then you can specify this using the 'source' argument. The relevant columns (Rf, Rb, Gf and Gb) are extracted automatically when 'source' is specified. For example RG <- read.maimages(files, source="genepix") is equivalent to the previous call. For more information on this function, try ?read.maimages or help.start() and take the 'Packages', 'limma' and '3.ReadingData' links. Best wishes, Matt Ritchie ************ PhD Student Division of Genetics and Bioinformatics The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville, 3050 VIC AUSTRALIA email: mritchie@wehi.edu.au web: http://bioinf.wehi.edu.au ************ Joyce Gu wrote: >Hello everyone, >I tried to use limma package to read cDNA data into R, I tried the samples >data >swirl, it all works, but my cDNA data is not the same as the sample data, my >data is tab-delimited .txt file, the header information is different from the >sample provided, I am wondering is any way I can manupiated the function to be >able to read customed data format with limma package, like pick up >colume="string", just as read.marrayRaw()? > >Any idea is greatly appreciated! > >******************************** >Joyce Gu M.S. >Scientific Programmer > >Cancer Genomics Group >Baylor College of Medicine >Phone: 832-824-4680 >Fax: 832-825-4038 >