I was trying to plot some data in R. I used the following code to draw a loess fit and got the output as>?lines(lowess(log(abs(t(res))), log(abs(t(synthesised)))), col="red")Error in lowess(log(abs(t(res))), log(abs(t(synthesised)))) :?? NA/NaN/Inf in foreign function call (arg 1) Then I thought to use your Limma package for background correction. Do you think it's a right choice ? However, I installed Limma using> source("http://www.bioconductor.org/biocLite.R") > biocLite("limma") > biocLite("statmod") > library(limma)and then used the commands which generated the error as follows --> system.time(fit <- loessFit( log(abs(t(res))), log(abs(t(synthesised)))))Error in loessFit(log(abs(t(res))), log(abs(t(synthesised)))) : ? binary operation on non-conformable arrays Timing stopped at: 0.57 0.06 0.64 NA NA> system.time(fit <- plotPrintTipLoess( log(abs(t(res))), log(abs(t(synthesised)))))Error in 1:layout$ngrid.c : NA/NaN argument In addition: Warning messages: 1: In object$printer : ? $ operator is invalid for atomic vectors, returning NULL 2: In object$M : $ operator is invalid for atomic vectors, returning NULL 3: In object$A : $ operator is invalid for atomic vectors, returning NULL 4: In object$M : $ operator is invalid for atomic vectors, returning NULL 5: In object$A : $ operator is invalid for atomic vectors, returning NULL 6: In layout$ngrid.c : ? $ operator is invalid for atomic vectors, returning NULL Timing stopped at: 0.66 0.01 0.67 NA NA Can someone please?tell me where the problem is and?what could be the right?command to use ? [[alternative HTML version deleted]]
I was trying to plot some data in R. I used the following code to draw a loess fit and got the output as>?lines(lowess(log(abs(t(res))), log(abs(t(synthesised)))), col="red")Error in lowess(log(abs(t(res))), log(abs(t(synthesised)))) :?? NA/NaN/Inf in foreign function call (arg 1) Then I thought to use Limma package for background correction. Is it a right choice ? However, I installed Limma using> source("http://www.bioconductor.org/biocLite.R") > biocLite("limma") > biocLite("statmod") > library(limma)and then used the commands which generated the error as follows --> system.time(fit <- loessFit( log(abs(t(res))), log(abs(t(synthesised)))))Error in loessFit(log(abs(t(res))), log(abs(t(synthesised)))) : ? binary operation on non-conformable arrays Timing stopped at: 0.57 0.06 0.64 NA NA> system.time(fit <- plotPrintTipLoess( log(abs(t(res))), log(abs(t(synthesised)))))Error in 1:layout$ngrid.c : NA/NaN argument In addition: Warning messages: 1: In object$printer : ? $ operator is invalid for atomic vectors, returning NULL 2: In object$M : $ operator is invalid for atomic vectors, returning NULL 3: In object$A : $ operator is invalid for atomic vectors, returning NULL 4: In object$M : $ operator is invalid for atomic vectors, returning NULL 5: In object$A : $ operator is invalid for atomic vectors, returning NULL 6: In layout$ngrid.c : ? $ operator is invalid for atomic vectors, returning NULL Timing stopped at: 0.66 0.01 0.67 NA NA Can someone please?tell me where the problem is and?what could [[alternative HTML version deleted]]
1. Please don't double post. 2. You probably have some "synthesized" values that are 0 and so get -Inf for their logs, which is NaN, thereby producing the error messages. Failing that, your data may be messed up in some way (character values, stray non-characters, ...) -- Bert Gunter -----Original Message----- From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of shetumi at aim.com Sent: Friday, May 30, 2008 7:32 AM To: r-help at r-project.org Subject: [R] loess plot I was trying to plot some data in R. I used the following code to draw a loess fit and got the output as>?lines(lowess(log(abs(t(res))), log(abs(t(synthesised)))), col="red")Error in lowess(log(abs(t(res))), log(abs(t(synthesised)))) :?? NA/NaN/Inf in foreign function call (arg 1) Then I thought to use your Limma package for background correction. Do you think it's a right choice ? However, I installed Limma using> source("http://www.bioconductor.org/biocLite.R") > biocLite("limma") > biocLite("statmod") > library(limma)and then used the commands which generated the error as follows --> system.time(fit <- loessFit( log(abs(t(res))), log(abs(t(synthesised)))))Error in loessFit(log(abs(t(res))), log(abs(t(synthesised)))) : ? binary operation on non-conformable arrays Timing stopped at: 0.57 0.06 0.64 NA NA> system.time(fit <- plotPrintTipLoess( log(abs(t(res))),log(abs(t(synthesised))))) Error in 1:layout$ngrid.c : NA/NaN argument In addition: Warning messages: 1: In object$printer : ? $ operator is invalid for atomic vectors, returning NULL 2: In object$M : $ operator is invalid for atomic vectors, returning NULL 3: In object$A : $ operator is invalid for atomic vectors, returning NULL 4: In object$M : $ operator is invalid for atomic vectors, returning NULL 5: In object$A : $ operator is invalid for atomic vectors, returning NULL 6: In layout$ngrid.c : ? $ operator is invalid for atomic vectors, returning NULL Timing stopped at: 0.66 0.01 0.67 NA NA Can someone please?tell me where the problem is and?what could be the right?command to use ? [[alternative HTML version deleted]] ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Hello R users: I was trying to draw a boxplot?using 2 variables (rain and wind). Both of them has length 25056. So dummy is a matrix with dimension 2 x 25056. First I tried to draw a full boxplot using the following code?and gave an error> boxplot(dummy$Rain~dummy$Wind)Error: cannot allocate vector of size 2.8 Gb In addition: Warning messages: 1: In rep.int(boxwex, n) : ? Reached total allocation of 1535Mb: see help(memory.size) 2: In rep.int(boxwex, n) : ? Reached total allocation of 1535Mb: see help(memory.size) 3: In rep.int(boxwex, n) : ? Reached total allocation of 1535Mb: see help(memory.size) 4: In rep.int(boxwex, n) : ? Reached total allocation of 1535Mb: see help(memory.size) and?thereafter I tried to draw boxplots at regular intervals (that means ) and that didnt work either> boxplot(dummy$Rain~cut(dummy$Wind,(1:25)*1000), data=dummy)Error in plot.window(xlim = xlim, ylim = ylim, log = log, yaxs = pars$yaxs) : ? need finite 'ylim' values In addition: Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 3: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 4: In min(x) : no non-missing arguments to min; returning Inf 5: In max(x) : no non-missing arguments to max; returning -Inf Also I used ?boxplot(dummy$Rain~cut(dummy$Wind, breaks=seq(from=1,to=25000,by=1000)), data=dummy) and that showing only sigle boxplot at far left corner. What would be the right ting to do ? [[alternative HTML version deleted]]