Took a day off from coding… Given my matrix.. these 2 blocks of code should have called different sets of results.. but the result of every (up/down) file is identical (now that I wrote them to excel and can look at them side by side… the topTable for each data set is different for each contrast so printing that and can sort in Excel. topTable(fit2, adjust="BH", n=20, coef=1, sort.by=”logFC”) #Bacteria - healthy tops <- topTable(fit2, n=Inf) # get all genes tops [which(tops$logFC > 0), ] [1:25,] # up reg top 25 write.table(tops, file="topsbacteria.txt") tops [which(tops$logFC < 0), ] [1:25,] # down reg top 25 write.table(tops, file="lowsbacteria.txt") topTable(fit2, adjust="BH", n=20, coef=2, sort.by=”logFC”) #phytoplasma - healthy tops <- topTable(fit2, n=Inf ) # get all genes tops[which(tops$logFC > 0), ] [1:25,] # up reg top 25 write.table(tops, file="topsphytoplasma.txt") tops[which(tops$logFC < 0), ] [1:25,] # down reg top 25 write.table(tops, file="lowsphytoplasma.txt") if I put a coef into the second line (for example) > topbacteria <- topTable(fit2, adjust="BH", n=20 coef=1) Error: unexpected symbol in "topsbacteria <- topTable(fit2, adjust="BH", n=20 coef" But thus all my resultant up and down regulated tables are the same…. Whether you think you can or think you can't - Your're right... Henry Ford Cristina Paul Citrus Quarantine Unit USDA-ARS-BA-PSI-MPPL Mailling address: Bldg 004 Rm 118 Beltsville MD 20705 office: 301-504-7657 FAX: 301-504-5449 Cell: 240-286-6709 Physical Address: Range 1 head house #6 From: seandavi@gmail.com<mailto:seandavi@gmail.com> [mailto:seandavi@gmail.com] On Behalf Of Sean Davis Sent: Tuesday, May 01, 2012 1:30 PM To: Paul, Cristina Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: Re: [BioC] How do I find up and down regulated genes for each contrast in LIMMA? On Tue, May 1, 2012 at 1:22 PM, Paul, Cristina <cristina.paul@ars.usda.gov<mailto:cristina.paul@ars.usda.gov>> wrote: R.2.14 in RStudio all packages up to date. Using the contrast.matrix I have been using lmfit etc from Limma, and have obtained a very informative Venn Diagram of our results (all trts minus healthy)... I would like to find the top 25 (in one trt only 5 genes were unique to the pathogen) up and down regulated genes... for each pathogen vs Healthy contrast. The code below gives me total across all the contrasts, or appears to. Have googled and read most of day but have found no code etc for doing this, or do I need to make a matrix for each comparison separately? I tried topTableF in the tops code (given topTableF provided the contrast data) but result was NA's... > design #each trt 4 CEL file replicates no subtreatments Virus Bacteria Healthy phytoplasma 1 0 1 0 0 2 0 1 0 0 3 0 1 0 0 4 0 1 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 0 0 0 9 0 0 1 0 10 0 0 1 0 11 0 0 1 0 12 0 0 1 0 13 0 0 0 1 14 0 0 0 1 15 0 0 0 1 16 0 0 0 1 fit <- lmFit(eset, design) contrast.matrix<-makeContrasts(Bacteria-Healthy, Phytoplasma-Healthy, Virus-Healthy, levels=design) fit2 <- contrasts.fit(fit, contrast.matrix) fit2 <- eBayes(fit2) topTable(fit2, adjust="BH", n=20) results<-decideTests(fit2) vennDiagram(results) topTableF(fit2, n=20) tops <- topTable(fit2, n=Inf) # all on chip You'll want to include the coef argument in the topTable call to specify which contrast you are examining. Sean tops[which(tops$logFC > 0), ] [1:25,] # up reg top 25 tops[which(tops$logFC < 0), ] [1:25,] # down reg top 25 thank you in advance for all help.... Whether you think you can or think you can't - Your're right... Henry Ford Cristina Paul This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]