Hi Rich, Richard Friedman wrote: > Jim and List, > > > On Jun 8, 2010, at 9:15 AM, James W. MacDonald wrote: > >> Hi Richard, >> >> Richard Friedman wrote: >>> Dear Bioconductor List, >>> I received an error message when trying to normalize data with >>> AgiMicroRMA >>> > agiMicro.rma=rmaMicroRna(agiMicroraw, >>> + normalize=TRUE, >>> + background=FALSE) >>> Error in if (min(dd.aux$Rb) < 0) { :H >>> missing value where TRUE/FALSE needed >>> > agiMicro.rma=rmaMicroRna(agiMicroraw, >>> + normalize=TRUE, >>> + background=TRUE) >>> Error in if (min(dd.aux$Rb) < 0) { : >>> missing value where TRUE/FALSE needed >> >> It looks like you have some NA values in agiMicroraw$Rb, so I would >> check that first. I don't see any code in rmaMicroRna() to gracefully >> handle missing data, so that is likely the problem. > > I didn't see any NAs in Rb but the maximum value of Rb was was 65535 > whereas the mean and median were 51 and 168 respectively. > Does this seem like a saturation effect? Probably. At least for Affy scanners the maximum is 2^16-1, so if you have a bunch of values at that level, I would imagine you have a saturation problem. > If so can mess up the program? > Also I note negative values for $R. > Can this mess up the program? > >> >> If there aren't any NA values in agiMicroraw$Rb, then you should try >> debuggind rmaMicroRna() to see where things are going wrong. Simply >> start with >> >> debug(rmaMicroRna) >> >> and then >> >> agiMicro.rma <- rmaMicroRna(agiMicroraw, TRUE, FALSE) >> >> you will then go into the browser, and can step through the function >> until you get to >> >> ProbeName.rep = >> unique(dd$genes$ProbeName[duplicated(dd$genes$ProbeName)]) >> dd.aux = dd[1:length(ProbeName.rep), ] >> >> at which time you can look for NA values in dd.aux$Rb, and try to >> track down where they come from. But looking at the code, I don't see >> any obvious way for them to be produced if not already there. > > Pasting from session: > #################################################################### ################## > > > debug: dd.aux = dd[1:length(ProbeName.rep), ] > Browse[2]> dd.aux$Rb > Error: object 'dd.aux' not found Heh. In the browser, the line debug: dd.aux = dd[1:length(ProbeName.rep), ] means that R is just about to process that line, not that it has already processed the line. So if you had hit enter, and then looked at dd.aux$Rb, then it would have output a bunch of data. Best, Jim > #################################################################### ################## > > > For some reason dd.aux was nor created. Can that be the problem? > > Thankls and best wishes, > Rich > > >> >> Best, >> >> Jim >> >> >>> > >>> ################################################################## ############## >>> >>> My session Inforrmation is: >>> > 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] AgiMicroRna_1.2.0 preprocessCore_1.10.0 >>> affy_1.26.1 limma_3.4.0 >>> [5] Biobase_2.8.0 >>> loaded via a namespace (and not attached): >>> [1] affyio_1.16.0 >>> > >>> ################################################################## ############## >>> >>> My session up to the attempt to normalize is: >>> ################################################################## ############### >>> >>> > targets<-readTargets("Targets.txt",verbose=TRUE) >>> Target File >>> FileName Treatment GErep >>> AxCNTx1x1x1 AxCNTx1x1x1.txt A.CNT 1 >>> AxCNTx2x2x2 AxCNTx2x2x2.txt A.CNT 1 >>> AxCNTx3x3x3 AxCNTx3x3x3.txt A.CNT 1 >>> AxCNTx7x4x4 AxCNTx7x4x4.txt A.CNT 1 >>> BxCCL4x1x1x5 BxCCL4x1x1x5.txt B.CCL4 2 >>> BxCCL4x2x2x6 BxCCL4x2x2x6.txt B.CCL4 2 >>> BxCCL4x3x3x7 BxCCL4x3x3x7.txt B.CCL4 2 >>> BxCCL4x5x4x8 BxCCL4x5x4x8.txt B.CCL4 2 >>> CxBDLx1x1x9 CxBDLx1x1x9.txt C.BDL 3 >>> CxBDLx2x2x10 CxBDLx2x2x10.txt C.BDL 3 >>> CxBDLx3x3x11 CxBDLx3x3x11.txt C.BDL 3 >>> CxBDLx4x4x12 CxBDLx4x4x12.txt C.BDL 3 >>> DxaHSCx1x1x13 DxaHSCx1x1x13.txt D.aHSC 4 >>> DxaHSCx2x2x14 DxaHSCx2x2x14.txt D.aHSC 4 >>> DxaHSCx3x3x15 DxaHSCx3x3x15.txt D.aHSC 4 >>> DxaHSCx4x4x16 DxaHSCx4x4x16.txt D.aHSC 4 >>> > agiMicroraw<-readMicroRnaAFE(targets,verbose=TRUE) >>> Read AxCNTx1x1x1.txt >>> Read AxCNTx2x2x2.txt >>> Read AxCNTx3x3x3.txt >>> Read AxCNTx7x4x4.txt >>> Read BxCCL4x1x1x5.txt >>> Read BxCCL4x2x2x6.txt >>> Read BxCCL4x3x3x7.txt >>> Read BxCCL4x5x4x8.txt >>> Read CxBDLx1x1x9.txt >>> Read CxBDLx2x2x10.txt >>> Read CxBDLx3x3x11.txt >>> Read CxBDLx4x4x12.txt >>> Read DxaHSCx1x1x13.txt >>> Read DxaHSCx2x2x14.txt >>> Read DxaHSCx3x3x15.txt >>> Read DxaHSCx4x4x16.txt >>> RGList: >>> dd$R: 'gTotalGeneSignal' >>> dd$G: 'gTotalProbeSignal' >>> dd$Rb: 'gMeanSignal' >>> dd$Gb: 'gProcessedSignal' >>> > agiMicro.rma=rmaMicroRna(agiMicroraw, >>> + normalize=TRUE, >>> + background=FALSE) >>> Error in if (min(dd.aux$Rb) < 0) { : >>> missing value where TRUE/FALSE needed >>> ################################################################## ############## >>> >>> Thanks and best wishes, >>> 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 >>> [[alternative HTML version deleted]] >>> _______________________________________________ >>> 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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

On Tue, Jun 8, 2010 at 10:56 PM, Richard Friedman <friedman at="" cancercenter.columbia.edu=""> wrote: > Jim and List, > > > On Jun 8, 2010, at 9:15 AM, James W. MacDonald wrote: > >> Hi Richard, >> >> Richard Friedman wrote: >>> >>> Dear Bioconductor List, >>> ? ? ? ?I received an error message when trying to normalize data with >>> ?AgiMicroRMA >>> > agiMicro.rma=rmaMicroRna(agiMicroraw, >>> + ? ? ? ? ? ? ? normalize=TRUE, >>> + ? ? ? ? ? ? ? background=FALSE) >>> Error in if (min(dd.aux$Rb) < 0) { : >>> ?missing value where TRUE/FALSE needed >>> > agiMicro.rma=rmaMicroRna(agiMicroraw, >>> + ? ? ? ? ? ? ? normalize=TRUE, >>> + ? ? ? ? ? ? ? background=TRUE) >>> Error in if (min(dd.aux$Rb) < 0) { : >>> ?missing value where TRUE/FALSE needed >> >> It looks like you have some NA values in agiMicroraw$Rb, so I would check >> that first. I don't see any code in rmaMicroRna() to gracefully handle >> missing data, so that is likely the problem. > > ? ? ? ?I didn't see any NAs in Rb but the maximum value of Rb was ?was 65535 > whereas the mean and median were 51 and 168 respectively. > Does this seem like ?a saturation effect? > If so can mess up the program? > Also I note negative values for $R. > Can this mess up the program? > >> >> If there aren't any NA values in agiMicroraw$Rb, then you should try >> debuggind rmaMicroRna() to see where things are going wrong. Simply start >> with >> >> debug(rmaMicroRna) >> >> and then >> >> agiMicro.rma <- rmaMicroRna(agiMicroraw, TRUE, FALSE) >> >> you will then go into the browser, and can step through the function until >> you get to >> >> ProbeName.rep = unique(dd$genes$ProbeName[duplicated(dd$genes$ProbeName)]) >> dd.aux = dd[1:length(ProbeName.rep), ] >> >> at which time you can look for NA values in dd.aux$Rb, and try to track >> down where they come from. But looking at the code, I don't see any obvious >> way for them to be produced if not already there. > > Pasting from session: > #################################################################### ################## > > debug: dd.aux = dd[1:length(ProbeName.rep), ] > Browse[2]> dd.aux$Rb > Error: object 'dd.aux' not found > #################################################################### ################## > > For some reason dd.aux was nor created. Can that be the problem? You have to press ENTER (nothing else) in order to evaluate "dd.aux = ..." when you see: > debug: dd.aux = dd[1:length(ProbeName.rep), ] > Browse[2]> and first then do: > Browse[2]> dd.aux$Rb EXAMPLE: > foo <- function() { a <- 1; b <- 2; } > debug(foo) > foo() debugging in: foo() debug: { a <- 1 b <- 2 } Browse[2]> debug: a <- 1 Browse[2]> a Error: object 'a' not found Browse[2]> a Error: object 'a' not found Browse[2]> a Error: object 'a' not found Browse[2]> # ENTER <= 'a <- 1' is evaluated here debug: b <- 2 Browse[2]> a [1] 1 Browse[2]> b Error: object 'b' not found Browse[2]> # ENTER <= 'b <- 2' is evaluated here exiting from: foo() > /Henrik > > Thankls and best wishes, > Rich > > >> >> Best, >> >> Jim >> >> >>> > >>> >>> ################################################################## ############## >>> My session Inforrmation is: >>> > 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] AgiMicroRna_1.2.0 ? ? preprocessCore_1.10.0 affy_1.26.1 >>> ?limma_3.4.0 >>> [5] Biobase_2.8.0 >>> loaded via a namespace (and not attached): >>> [1] affyio_1.16.0 >>> > >>> >>> ################################################################## ############## >>> My session up to the attempt to normalize is: >>> >>> ################################################################## ############### >>> > targets<-readTargets("Targets.txt",verbose=TRUE) >>> Target File >>> ? ? ? ? ? ? ? ? ? ? ? FileName Treatment GErep >>> AxCNTx1x1x1 ? ? AxCNTx1x1x1.txt ? ? A.CNT ? ? 1 >>> AxCNTx2x2x2 ? ? AxCNTx2x2x2.txt ? ? A.CNT ? ? 1 >>> AxCNTx3x3x3 ? ? AxCNTx3x3x3.txt ? ? A.CNT ? ? 1 >>> AxCNTx7x4x4 ? ? AxCNTx7x4x4.txt ? ? A.CNT ? ? 1 >>> BxCCL4x1x1x5 ? BxCCL4x1x1x5.txt ? ?B.CCL4 ? ? 2 >>> BxCCL4x2x2x6 ? BxCCL4x2x2x6.txt ? ?B.CCL4 ? ? 2 >>> BxCCL4x3x3x7 ? BxCCL4x3x3x7.txt ? ?B.CCL4 ? ? 2 >>> BxCCL4x5x4x8 ? BxCCL4x5x4x8.txt ? ?B.CCL4 ? ? 2 >>> CxBDLx1x1x9 ? ? CxBDLx1x1x9.txt ? ? C.BDL ? ? 3 >>> CxBDLx2x2x10 ? CxBDLx2x2x10.txt ? ? C.BDL ? ? 3 >>> CxBDLx3x3x11 ? CxBDLx3x3x11.txt ? ? C.BDL ? ? 3 >>> CxBDLx4x4x12 ? CxBDLx4x4x12.txt ? ? C.BDL ? ? 3 >>> DxaHSCx1x1x13 DxaHSCx1x1x13.txt ? ?D.aHSC ? ? 4 >>> DxaHSCx2x2x14 DxaHSCx2x2x14.txt ? ?D.aHSC ? ? 4 >>> DxaHSCx3x3x15 DxaHSCx3x3x15.txt ? ?D.aHSC ? ? 4 >>> DxaHSCx4x4x16 DxaHSCx4x4x16.txt ? ?D.aHSC ? ? 4 >>> > agiMicroraw<-readMicroRnaAFE(targets,verbose=TRUE) >>> Read AxCNTx1x1x1.txt >>> Read AxCNTx2x2x2.txt >>> Read AxCNTx3x3x3.txt >>> Read AxCNTx7x4x4.txt >>> Read BxCCL4x1x1x5.txt >>> Read BxCCL4x2x2x6.txt >>> Read BxCCL4x3x3x7.txt >>> Read BxCCL4x5x4x8.txt >>> Read CxBDLx1x1x9.txt >>> Read CxBDLx2x2x10.txt >>> Read CxBDLx3x3x11.txt >>> Read CxBDLx4x4x12.txt >>> Read DxaHSCx1x1x13.txt >>> Read DxaHSCx2x2x14.txt >>> Read DxaHSCx3x3x15.txt >>> Read DxaHSCx4x4x16.txt >>> ?RGList: >>> ? ? ? ?dd$R: ? ? ? ? ? 'gTotalGeneSignal' >>> ? ? ? ?dd$G: ? ? ? ? ? 'gTotalProbeSignal' >>> ? ? ? ?dd$Rb: ? ? ? ? ?'gMeanSignal' >>> ? ? ? ?dd$Gb: ? ? ? ? ?'gProcessedSignal' >>> > agiMicro.rma=rmaMicroRna(agiMicroraw, >>> + ? ? ? ? ? ? ? normalize=TRUE, >>> + ? ? ? ? ? ? ? background=FALSE) >>> Error in if (min(dd.aux$Rb) < 0) { : >>> ?missing value where TRUE/FALSE needed >>> >>> ################################################################## ############## >>> Thanks and best wishes, >>> 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 >>> ? ? ? ?[[alternative HTML version deleted]] >>> _______________________________________________ >>> 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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not >> be used for urgent or sensitive issues > > _______________________________________________ > 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 >