> > On Apr 30, 2010, at 3:08 PM, Heidi Dvinge wrote: > >>> >>> On Apr 30, 2010, at 2:42 PM, Heidi Dvinge wrote: >>> >>>> Hello Mike, >>>> >>>>> Greetings >>>>> >>>>> I have R 2.11, BioC 2.6 and HTqPCR 1.2 (see session info at the >>>>> end). >>>>> >>>>> I created a qPCRset object by using rbind() to concatenate four >>>>> pairs >>>>> of dissimilar cards for each experimental condition and then >>>>> cbind() >>>>> to concatenate the four objects into one: >>>>> >>>>> WT_time1.a | >>>>> WT_time1.b |---> WT_time1 >>>>> MT_time1.a | >>>>> MT_time1.b |---> MT_time1 >>>>> WT_time2.a | ---> s2010004660 >>>>> WT_time2.b |---> WT_time2 >>>>> MT_time2.a | >>>>> MT_time2.b |---> MT_time2 >>>>> >>>>> I set g <- c("MammU6") which is a endogenous control gene. >>>>> >>>>> I then tried to plotCtOverview(s2010004660, genes=g, >>>>> groups=sampleNames(qPCRset), conf.int=TRUE) and got >>>>> >>>>>> plotCtOverview(s2010004660, genes=g, conf.int=TRUE) >>>>> Error in if (del == 0 && to == 0) return(to) : >>>>> missing value where TRUE/FALSE needed >>>>> >>>>> Here's the object info: >>>>> >>>>>> s2010004660 >>>>> An object of class "qPCRset" >>>>> Size: 768 features, 4 samples >>>>> Feature types: Endogenous Control, Target >>>>> Feature names: mmu-let-7b-4373168 mmu-let-7c-4373167 mmu- >>>>> let-7d-4395394 ... >>>>> Feature classes: >>>>> Feature categories: OK, Undetermined >>>>> Sample names: WT_4wks MT_4wks WT_17wks ... >>>>> >>>>> Could it be that the Feature classes slot is empty? >>>>> >>>> Feature classes shouldn't matter at all here. I can reproduce this >>>> using >>>> the data sets included in HTqPCR (qPCRraw and qPCRpros) though. What >>>> does >>>> traceback() say? And does the same happen when you use >>>> conf.int=FALSE? >>> >>> Thanks Heidi >>> >>> Here's the traceback(): >>> >>>> plotCtOverview(s2010004660, genes=g, conf.int=TRUE) >>> Error in if (del == 0 && to == 0) return(to) : >>> missing value where TRUE/FALSE needed >>>> traceback() >>> 3: seq.default(1.5, ncol(SD) * (nrow(SD) + 1), nrow(SD) + 1) >>> 2: seq(1.5, ncol(SD) * (nrow(SD) + 1), nrow(SD) + 1) >>> 1: plotCtOverview(s2010004660, genes = g, conf.int = TRUE) >>> >>> conf.int = FALSE it makes the plot without complaining. Actually, it >>> makes the plot in the first case, too, it just doesn't draw error >>> bars. >>> >> Hm, so for some reason it can't calculate a standard deviation for >> your >> qPCRset. However it should work even if SD returns NA. >> >> Do your have replicate genes in your set? And what happens if you >> say e.g. >> groups=c("A", "A", "B", "B")? > Heidi > > I see the same problem. > > > plotCtOverview(s2010004660, genes=g, > groups=c("WT_4wks"),conf.int=TRUE,replicates=TRUE) > Error in if (del == 0 && to == 0) return(to) : > missing value where TRUE/FALSE needed > > plotCtOverview(s2010004660, genes=g, > groups=c("WT_4wks","MT_4wks"),conf.int=TRUE,replicates=TRUE) > Error in if (del == 0 && to == 0) return(to) : > missing value where TRUE/FALSE needed > Just for the record, "group" needs a vector the same length as your number of samples, so in your case it should be c("WT_4wks","MT_4wks", "MT_17wks", "MT_17wks"). I'll add a warning about that in plotCtOverview, but I don't think that's the cause of the problem here. What do you get if you say summary(s2010004660)? I can't reproduce this behaviour with any of the data I have, but if you don't mind sending my your qPCRset (off list), then perhaps I can have a lot at if directly. \Heidi > It makes a plot but without error bars. > > Yes, there are replicates: > > Each card (stock ABI item) has 4 duplicates of the control. > > > exprs(s2010004660)[grep("U6",featureNames(s2010004660)),] > WT_4wks MT_4wks WT_17wks MT_17wks > MammU6-4395470 17.06939 17.18261 17.31673 17.11643 > MammU6-4395470 17.15968 17.25446 17.31998 17.10729 > MammU6-4395470 17.06865 17.07786 17.22182 17.02346 > MammU6-4395470 17.20133 17.17483 17.11134 16.96466 > MammU6-4395470 17.99183 17.92814 18.57421 18.11891 > MammU6-4395470 17.72530 17.83194 18.60460 17.95789 > MammU6-4395470 17.98547 17.90774 18.75409 18.00277 > MammU6-4395470 17.88600 17.96328 18.40904 18.12783 > > With stats: > > > colMeans(exprs(s2010004660)[grep("U6",featureNames(s2010004660)),]) > WT_4wks MT_4wks WT_17wks MT_17wks > 17.51096 17.54011 17.91398 17.55241 > > sd(exprs(s2010004660)[grep("U6",featureNames(s2010004660)),]) > WT_4wks MT_4wks WT_17wks MT_17wks > 0.4230635 0.3975762 0.7266933 0.5388762 > > Mike > >> >> \Heidi >> >>> Thanks again for the package and the help >>> >>> Mike >>>> >>>> \Heidi >>>> >>>>> Here's session info: >>>>> >>>>>> sessionInfo() >>>>> R version 2.11.0 (2010-04-22) >>>>> 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_1.2.0 limma_3.4.0 RColorBrewer_1.0-2 >>>>> Biobase_2.8.0 MASS_7.3-5 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affy_1.26.0 affyio_1.16.0 gdata_2.7.1 >>>>> gplots_2.7.4 gtools_2.6.1 preprocessCore_1.10.0 >>>>> [7] tools_2.11.0 >>>>> >>>>> Thanks >>>>> >>>>> Mike >>>>> >>>>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> >>> 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 >>> >>> >>> >>> >>> >> >> > > 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 > > > > >

On May 2, 2010, at 3:26 AM, Heidi Dvinge wrote: >> >> On Apr 30, 2010, at 3:08 PM, Heidi Dvinge wrote: >> >>>> >>>> On Apr 30, 2010, at 2:42 PM, Heidi Dvinge wrote: >>>> >>>>> Hello Mike, >>>>> >>>>>> Greetings >>>>>> >>>>>> I have R 2.11, BioC 2.6 and HTqPCR 1.2 (see session info at the >>>>>> end). >>>>>> >>>>>> I created a qPCRset object by using rbind() to concatenate four >>>>>> pairs >>>>>> of dissimilar cards for each experimental condition and then >>>>>> cbind() >>>>>> to concatenate the four objects into one: >>>>>> >>>>>> WT_time1.a | >>>>>> WT_time1.b |---> WT_time1 >>>>>> MT_time1.a | >>>>>> MT_time1.b |---> MT_time1 >>>>>> WT_time2.a | ---> s2010004660 >>>>>> WT_time2.b |---> WT_time2 >>>>>> MT_time2.a | >>>>>> MT_time2.b |---> MT_time2 >>>>>> >>>>>> I set g <- c("MammU6") which is a endogenous control gene. >>>>>> >>>>>> I then tried to plotCtOverview(s2010004660, genes=g, >>>>>> groups=sampleNames(qPCRset), conf.int=TRUE) and got >>>>>> >>>>>>> plotCtOverview(s2010004660, genes=g, conf.int=TRUE) >>>>>> Error in if (del == 0 && to == 0) return(to) : >>>>>> missing value where TRUE/FALSE needed >>>>>> >>>>>> Here's the object info: >>>>>> >>>>>>> s2010004660 >>>>>> An object of class "qPCRset" >>>>>> Size: 768 features, 4 samples >>>>>> Feature types: Endogenous Control, Target >>>>>> Feature names: mmu-let-7b-4373168 mmu-let-7c-4373167 mmu- >>>>>> let-7d-4395394 ... >>>>>> Feature classes: >>>>>> Feature categories: OK, Undetermined >>>>>> Sample names: WT_4wks MT_4wks WT_17wks ... >>>>>> >>>>>> Could it be that the Feature classes slot is empty? >>>>>> >>>>> Feature classes shouldn't matter at all here. I can reproduce this >>>>> using >>>>> the data sets included in HTqPCR (qPCRraw and qPCRpros) though. >>>>> What >>>>> does >>>>> traceback() say? And does the same happen when you use >>>>> conf.int=FALSE? >>>> >>>> Thanks Heidi >>>> >>>> Here's the traceback(): >>>> >>>>> plotCtOverview(s2010004660, genes=g, conf.int=TRUE) >>>> Error in if (del == 0 && to == 0) return(to) : >>>> missing value where TRUE/FALSE needed >>>>> traceback() >>>> 3: seq.default(1.5, ncol(SD) * (nrow(SD) + 1), nrow(SD) + 1) >>>> 2: seq(1.5, ncol(SD) * (nrow(SD) + 1), nrow(SD) + 1) >>>> 1: plotCtOverview(s2010004660, genes = g, conf.int = TRUE) >>>> >>>> conf.int = FALSE it makes the plot without complaining. Actually, >>>> it >>>> makes the plot in the first case, too, it just doesn't draw error >>>> bars. >>>> >>> Hm, so for some reason it can't calculate a standard deviation for >>> your >>> qPCRset. However it should work even if SD returns NA. >>> >>> Do your have replicate genes in your set? And what happens if you >>> say e.g. >>> groups=c("A", "A", "B", "B")? >> Heidi >> >> I see the same problem. >> >>> plotCtOverview(s2010004660, genes=g, >> groups=c("WT_4wks"),conf.int=TRUE,replicates=TRUE) >> Error in if (del == 0 && to == 0) return(to) : >> missing value where TRUE/FALSE needed >>> plotCtOverview(s2010004660, genes=g, >> groups=c("WT_4wks","MT_4wks"),conf.int=TRUE,replicates=TRUE) >> Error in if (del == 0 && to == 0) return(to) : >> missing value where TRUE/FALSE needed >> > Just for the record, "group" needs a vector the same length as your > number > of samples, so in your case it should be c("WT_4wks","MT_4wks", > "MT_17wks", "MT_17wks"). I'll add a warning about that in > plotCtOverview, > but I don't think that's the cause of the problem here. What do you > get if > you say summary(s2010004660)? Hi Heidi I don't understand the purpose and function of 'group'. What would be the effect, for example, of having four identical sample labels? I tried using the default and I tried setting it to the sample IDs (all four) and got the same error. > > I can't reproduce this behaviour with any of the data I have, but if > you > don't mind sending my your qPCRset (off list), then perhaps I can > have a > lot at if directly. I'll send it off directly. Thanks Mike > > \Heidi > >> It makes a plot but without error bars. >> >> Yes, there are replicates: >> >> Each card (stock ABI item) has 4 duplicates of the control. >> >>> exprs(s2010004660)[grep("U6",featureNames(s2010004660)),] >> WT_4wks MT_4wks WT_17wks MT_17wks >> MammU6-4395470 17.06939 17.18261 17.31673 17.11643 >> MammU6-4395470 17.15968 17.25446 17.31998 17.10729 >> MammU6-4395470 17.06865 17.07786 17.22182 17.02346 >> MammU6-4395470 17.20133 17.17483 17.11134 16.96466 >> MammU6-4395470 17.99183 17.92814 18.57421 18.11891 >> MammU6-4395470 17.72530 17.83194 18.60460 17.95789 >> MammU6-4395470 17.98547 17.90774 18.75409 18.00277 >> MammU6-4395470 17.88600 17.96328 18.40904 18.12783 >> >> With stats: >> >>> colMeans(exprs(s2010004660)[grep("U6",featureNames(s2010004660)),]) >> WT_4wks MT_4wks WT_17wks MT_17wks >> 17.51096 17.54011 17.91398 17.55241 >>> sd(exprs(s2010004660)[grep("U6",featureNames(s2010004660)),]) >> WT_4wks MT_4wks WT_17wks MT_17wks >> 0.4230635 0.3975762 0.7266933 0.5388762 >> >> Mike >> >>> >>> \Heidi >>> >>>> Thanks again for the package and the help >>>> >>>> Mike >>>>> >>>>> \Heidi >>>>> >>>>>> Here's session info: >>>>>> >>>>>>> sessionInfo() >>>>>> R version 2.11.0 (2010-04-22) >>>>>> 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_1.2.0 limma_3.4.0 RColorBrewer_1.0-2 >>>>>> Biobase_2.8.0 MASS_7.3-5 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affy_1.26.0 affyio_1.16.0 gdata_2.7.1 >>>>>> gplots_2.7.4 gtools_2.6.1 preprocessCore_1.10.0 >>>>>> [7] tools_2.11.0 >>>>>> >>>>>> Thanks >>>>>> >>>>>> Mike >>>>>> >>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> >>>> 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 >>>> >>>> >>>> >>>> >>>> >>> >>> >> >> 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 >> >> >> >> >> > > 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