similar to: SAMseq errors

Sorry forgot to use plain text format, hope this time it works: Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error: > library(samr) Loading required package: impute Loading required package: matrixStats Attaching package: ?matrixStats? The following objects are masked from

I'm having trouble with the order of the panels using xyplot. I had used this bit of code before and received the desired plot (the code was not identical, but very similar; perhaps more importantly I was working with an older version of R) . Now the panels appear right to left instead of left to right, as it says in the help files, which is what I would like. Does anyone know if this has

Hi, I'm just following your messages the overhead that the code for dealing with possible NA/NaN values brings. When I was setting up part of the matrixStats package, I've also though about this. I was thinking of having an additional logical argument 'hasNA'/'has.na' where you as a user can specify whether there is NA/NaN:s or not, allowing the code to avoid it or not.

Hi Everybody, I am having a problem with loading Biobase package. I typed 2 lines below at R prompt > source ("http://boconductor.org/biocLite.R") > biocLite (lib="/usr/local/lib/R/library") which attempted to install a bunch of packages with varying degree of success. Out of 29, 13 failed. Biobase is one of them. As a matter of fact, when I looked at logs, most

Hi, is there a hasNA() / an anyNA() function in R? Of course, hasNA <- function(x) { any(is.na(x)); } would do, but that would scan all elements in 'x' and then do the test. I'm looking for a more efficient implementation that returns TRUE at the first NA, e.g. hasNA <- function(x) { for (kk in seq(along=x)) { if (is.na(x[kk])) return(TRUE); } FALSE; }

A new release 0.13.1 of matrixStats is now on CRAN [http://cran.r-project.org/package=matrixStats]. The source code is available on GitHub [https://github.com/HenrikBengtsson/matrixStats]. WHAT DOES IT DO? The matrixStats package provides highly optimized functions for computing common summaries over rows and columns of matrices, e.g.rowQuantiles(). There are also functions that operate on

A new release 0.13.1 of matrixStats is now on CRAN [http://cran.r-project.org/package=matrixStats]. The source code is available on GitHub [https://github.com/HenrikBengtsson/matrixStats]. WHAT DOES IT DO? The matrixStats package provides highly optimized functions for computing common summaries over rows and columns of matrices, e.g.rowQuantiles(). There are also functions that operate on

Just following up on this old thread since matrixStats 0.53.0 is now out, which supports this use case: > x <- rep(TRUE, times = 2^31) > y <- sum(x) > y [1] NA Warning message: In sum(x) : integer overflow - use sum(as.numeric(.)) > y <- matrixStats::sum2(x, mode = "double") > y [1] 2147483648 > str(y) num 2.15e+09 No coercion is taking place, so the

Hi. On Sun, Feb 13, 2011 at 10:18 AM, TakeoKatsuki <takeo.katsuki at gmail.com> wrote: > > Hi Henrik, > > It would be nice if functions of the matrixStats package can handle array > data. > For example, rowSums() of the base package sums along the third axis of an > array by rowSums(x, dim=2). That is a good idea. This was indeed the initial objective before starting

It looks like OP uses a data.frame, so in order to use matrixStats (I'm the author) one would have to pay the price to coerce to a matrix before using matrixStats::rowMaxs(). However, if it is that the original data could equally well live in a matrix, then matrixStats should be computational efficient for this task. (I've seen cases where an original matrix was turned into a data.frame

On Tue, Feb 20, 2018 at 11:58 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote: > Ista, et. al: efficiency? > (Note: I needed to correct my previous post: do.call() is required for > pmax() over the data frame) > > > x <- data.frame(matrix(runif(12e6), ncol=12)) > > > system.time(r1 <- do.call(pmax,x)) > user system elapsed > 0.049 0.000

Does anyone know if it is possible to add a dictionary file of known words that becomes part of the *built* package to tell 'R CMD check --as-cran' not to report these words as misspelled. I want this dictionary to come with the *.tar.gz such that it will be available regardless where the package is checked. For instance, currently I get: * using log directory

Hi Martin, Henrik, Thanks for the follow up. @Martin: I vote for 2) without *any* hesitation :-) (and uniformity could be restored at some point in the future by having prod(), rowSums(), colSums(), and others align with the behavior of length() and sum()) Cheers, H. On 01/27/2018 03:06 AM, Martin Maechler wrote: >>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com>

>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com> >>>>> on Thu, 25 Jan 2018 09:30:42 -0800 writes: > Just following up on this old thread since matrixStats 0.53.0 is now > out, which supports this use case: >> x <- rep(TRUE, times = 2^31) >> y <- sum(x) >> y > [1] NA > Warning message:

> On Wednesday, May 20, 2020, 7:00:09 AM EDT, peter dalgaard <pdalgd at gmail.com> wrote: > > Expected, see FAQ 7.31. > > You just can't trust == on FP operations. Notice also Additionally, since you're implementing a "mean" function you are testing against R's mean, you might want to consider that R uses a two-pass calculation[1] to reduce floating

>>>>> Herv? Pag?s <hpages at fredhutch.org> >>>>> on Tue, 30 Jan 2018 13:30:18 -0800 writes: > Hi Martin, Henrik, > Thanks for the follow up. > @Martin: I vote for 2) without *any* hesitation :-) > (and uniformity could be restored at some point in the > future by having prod(), rowSums(), colSums(), and others >

Hi, I have a long numeric vector 'xx' and I want to use sum() to count the number of elements that satisfy some criteria like non-zero values or values lower than a certain threshold etc... The problem is: sum() returns an NA (with a warning) if the count is greater than 2^31. For example: > xx <- runif(3e9) > sum(xx < 0.9) [1] NA Warning message: In sum(xx

On Windows there are a few 'pthreads' implementation, e.g. pthreads-w32 and winpthreads [https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Using-pthreads]. We're thinking of giving them a try for the matrixStats package, and basic tests indicates it works, but since Windows pthreads are not used by core R (or?) I've got a little bit worried that we will face overwhelming

Hola Jorge, muchas gracias por tu pronta respuesta, no me di cuenta que el formateo podría causar problemas, envío de nuevo el código sin formatos. La idea básica es para un set de números de columnas (desordenados) y un set de numeros de fila el loop lo que hace es ir a la fila y columna correspondiente de data, tomar el valor y luego hacer la media sobre esos.

Aaaah ... and argh - I should have better not to post R question at midnight, especially when I know it forks the process and it's not using threads. Brain meltdown. (So, we'll proceed trying to use pthreads in matrixStats also for Windows). Sorry for the noise and thanks Kasper. Henrik On Aug 15, 2015 02:52, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com> wrote: