On Apr 21, 2010, at 2:46 PM, Heidi Dvinge wrote: > Hello Mike, > > the current HTqPCR version is actually 1.1.4, c.f. > http://www.ebi.ac.uk/bertone/software.html > > That's in the R development version, so it'll be automatically > installed > if you have R-2.11. Technically it should also run with R-2.10 (at > least > it works on my laptop), but since mixing package and R versions is > generally strongly discouraged, doing so is at your own risk. > > I don't recall having made any changes to plotCtOverview though. Can > you > perhaps send the exact command you used? > > Regards > \Heidi Heidi Thanks for the reply. I will install the 2.11 version of R. (My 2.10 install says it's current.) Here's the command: plotCtOverview(x,groups=sampleNames(x),replicates=TRUE,conf.int=TRUE) It puts the first set of error bars in the correct place, but the second set of error bars overlaps white space and the spacing between error bars is less than the spacing between the main bars. It's as though the SD_ bars that included are throwing off the scale. I can send you a PDF of the image if you like. x is a subset containing the official endogenous control (MammU6) and several other small RNAs with multiple copies from a qPCRset object that I made by hand (I explain how below) from 7900HT files. I can send you a copy of this, too, if you like. I made the object from 7900HT mouse miRNA files I obtained from the RQ Manager package of SDS v2.3: s2010004660_A <- read.delim("~/Windows_Share/2010004660_A_results.txt", header=TRUE, sep="\t", na.string="Undetermined", skip=36) s2010004660_B <- read.delim("~/Windows_Share/2010004660_B_results.txt", header=TRUE, sep="\t", na.string="Undetermined", skip=36) {more lines like the above omitted} wt_4_x <- c(s2010004660_A$Ct,s2010004660_B$Ct) mt_4_x <- c(s2010004660_C$Ct,s2010004660_D$Ct) wt_17_x <- c(s2010004660_E$Ct,s2010004660_F$Ct) mt_17_x <- c(s2010004660_G$Ct,s2010004660_Ha$Ct) wt_4_feats <- factor(c(as.character(s2010004660_A $Detector),as.character(s2010004660_B$Detector))) mt_4_feats <- factor(c(as.character(s2010004660_C $Detector),as.character(s2010004660_D$Detector))) wt_17_feats <- factor(c(as.character(s2010004660_E $Detector),as.character(s2010004660_F$Detector))) mt_17_feats <- factor(c(as.character(s2010004660_G $Detector),as.character(s2010004660_Ha$Detector))) qs2010004660 <- new("qPCRset", exprs=exprs) featureNames(qs2010004660) <- sub("-[[:digit:]]* $","",wt_4_feats,perl=TRUE) featureType(qs2010004660) <- wt_4_tasks sampleNames(qs2010004660) <- c("WT_4wks", "MT_4wks", "WT_17wks", "MT_17wks") The plates (which I assume are stock items from ABI) are unusual relative to what I know from the HTpPCR documentation in that each treatment consists of two distinct plates. Plate 1 has unique miRNA targets and 4 endogenous control duplicates (MammU6). Plate 2 has a couple of hundred miRNA targets in duplicate and the same endogenous control. I can send you the layout if I haven't explained it well enough. The plot illustrates the point I'm trying to make that the expression of the controls is reasonably constant across the treatments, but I can't get the layout right. Thanks Mike >> Greetings >> >> I have a problem with the axis scale for the main bar being different >> than that for the error bars, i.e., the error bars don't line up over >> the signal bars. I was checking this list for this problem and saw >> that HTqPCR release version is apparently up to version 1.1.0 whereas >> the bioconductor site shows 1.0.0. Maybe the new release would fix >> the >> problem, but where would I get it? Updating didn't change the >> version. >> I also am getting main bars of the form SD_myGroups, which I assume >> is >> standard deviation. Can I turn this off? >> >> Thanks >> >> Mike >> >> R version 2.10.1 (2009-12-14) >> i386-apple-darwin9.8.0 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] HTqPCR_1.0.0 limma_3.2.3 RColorBrewer_1.0-2 >> Biobase_2.6.1 >> >> loaded via a namespace (and not attached): >> [1] affy_1.24.2 affyio_1.14.0 gdata_2.7.1 >> gplots_2.7.4 gtools_2.6.1 preprocessCore_1.8.0 >> [7] tools_2.10.1 >> >> >> Michael Muratet, Ph.D. >> Senior Scientist >> HudsonAlpha Institute for Biotechnology >> mmuratet at hudsonalpha.org >> (256) 327-0473 (p) >> (256) 327-0966 (f) >> >> Room 4005 >> 601 Genome Way >> Huntsville, Alabama 35806 >> >> _______________________________________________ >> 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 >> > > Michael Muratet, Ph.D. Senior Scientist HudsonAlpha Institute for Biotechnology mmuratet at hudsonalpha.org (256) 327-0473 (p) (256) 327-0966 (f) Room 4005 601 Genome Way Huntsville, Alabama 35806