Hi, I just have a quick question. I have been using limma to create toptables looking at differences betwen 6 groups. When I look at the results of the toptables I assumed that positive logFC meant that the gene was upregulated and if negative then it was down regulated. Is this correct? The reason that I ask is because I was doing some similar statistics using MEV software but the FC was the opposite way around. I have given an example below: group1 - group2 in limma gene X = +, Y=+ and Z=- in MEV gene X= - , Y= - and Z=+ Similar genes are detected but now im unsure as to whether or not they are up regulated in the first or second group. Please can someone help me with this. Thank you in advance. Best wishes, Katie

Katie, ------------------------------------------------------------ On Jun 16, 2010, at 4:36 PM, Richard Friedman wrote: > > On Jun 16, 2010, at 12:30 PM, Taylor, Katie wrote: > >> Hi, >> >> I just have a quick question. I have been using limma to create >> toptables looking at differences betwen 6 groups. When I look at >> the results of the toptables I assumed that positive logFC meant >> that the gene was upregulated and if negative then it was down >> regulated. Is this correct? logFC in limma means expression experiment > expression control if the contrast matrix is set up to represent experimenr-control. You can check this by hand in an excel spreadsheet of the output, normalized expression values. I am sorry but I haven''t used MEV and can't answer about it. I hope this helps, Rich Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ In Memoriam, George Scithers >> The reason that I ask is because I was doing some similar >> statistics using MEV software but the FC was the opposite way >> around. I have given an example below: >> >> group1 - group2 >> >> in limma gene X = +, Y=+ and Z=- >> in MEV gene X= - , Y= - and Z=+ >> >> Similar genes are detected but now im unsure as to whether or not >> they are up regulated in the first or second group. Please can >> someone help me with this. >> >> Thank you in advance. >> >> Best wishes, >> >> Katie >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Hi Katie Can you post the code you used in limma, and specifically, the design and contrast (if there was one) matrices Mick ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Taylor, Katie [kt70@leicester.ac.uk] Sent: 16 June 2010 17:30 To: bioconductor at stat.math.ethz.ch Subject: [BioC] question about limma Hi, I just have a quick question. I have been using limma to create toptables looking at differences betwen 6 groups. When I look at the results of the toptables I assumed that positive logFC meant that the gene was upregulated and if negative then it was down regulated. Is this correct? The reason that I ask is because I was doing some similar statistics using MEV software but the FC was the opposite way around. I have given an example below: group1 - group2 in limma gene X = +, Y=+ and Z=- in MEV gene X= - , Y= - and Z=+ Similar genes are detected but now im unsure as to whether or not they are up regulated in the first or second group. Please can someone help me with this. Thank you in advance. Best wishes, Katie _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor