Dear Sir/Madam, I am an user of limma and I used it to analyze two channel Agilent microarray before. However I have new two channel Agilent microarray data now which is different with what I analyzed before. It has separate green and red channels (in two files). It seems I can not use limma directly. I wonder is there any old version of limma can be used to deal with this kind of data, because the data I just got is generated in 2006. In the attachment is the header of the microarray data. Thanks in advance. Regards, Hui Jia, Ph.D. Post-Doctoral Fellow Lipovich lab Center for Molecular Medicine and Genetics School of Medicine Wayne State University 540 E. Canfield St. 3238 Scott Hall Detroit, MI 48201-1928 U.S.A. hjia at med.wayne.edu Office Phone +1 313-577-9637, Fax +1 313 577 5218

---------- Forwarded message ---------- Date: Fri, 17 Aug 2012 10:39:22 +1000 (AUS Eastern Standard Time) From: Gordon K Smyth <smyth@wehi.edu.au> To: "Jia, Hui" <hjia at="" med.wayne.edu=""> Subject: Re: question for limma Dear Hui Jia, I've never seen data in this format, so limma has never supported it directly. You could use limma read.maimages() to read in the red and green channels separately, then cbind them together, although this would require a little bit of R programming. Best wishes Gordon --------------------------------------------- Professor Gordon K Smyth, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3052, Australia. http://www.statsci.org/smyth On Thu, 16 Aug 2012, Jia, Hui wrote: > Dear Gordon, > > I am an user of limma and I used it to analyze two channel Agilent microarray > before. However I have new two channel Agilent microarray data now which is > different with what I analyzed before. It has separate green and red channels > (in two files). It seems I can not use limma directly. I wonder is there any > old version of limma can be used to deal with this kind of data, because the > data I just got is generated in 2006. In the attachment is the header of the > microarray data. Thanks in advance. > > Regards, > > Hui Jia, Ph.D. > Post-Doctoral Fellow > Lipovich lab > Center for Molecular Medicine and Genetics > School of Medicine > Wayne State University > 540 E. Canfield St. > 3238 Scott Hall > Detroit, MI 48201-1928 > U.S.A. > > hjia at med.wayne.edu > Office Phone +1 313-577-9637, Fax +1 313 577 5218 > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}