similar to: [BioC] oligo ids

Dear list, I am having a set of human oligo ids (H200006022 H200002025 H300004703 H200000442 H200005719 H300018350) which I want to map to Ensembl or RefSeq. I am sure R has a function to do that. I downloaded the {oligo} package and tried to use the probeNames function. Although the factor of ologo ids is an object (as the argument to probeNames should be) I retrieve the following error:

Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many

> I have a code that has several probes with the same probename. When I define the probe to use a translator and then try to match for all the occurances of the probename in a D script I get the following error: > > dtrace: invalid probe specifier mpi__test$target:::RECV_REQ_ACT_EV { printf("%d %d", args[0]->bar, args[0]->baz); }: in action list: args[ ] may not be

Dear Help, After loading the pd.Citrus library and checking the DataFrame, I ran > the R code for: > > 1) 'oligo' > > > > {> library(pd.citrus) > Loading required package: RSQLite > Loading required package: DBI > > data(pmSequence) > > > show(pmSequence) > DataFrame with 341730 rows and 2 columns > fid sequence > <integer>

Dear All, I am analyzing the miRNA data set in which I have 817 unique probes for each they have 20 features each . I have to group the similar features and take the median across them so that I have a data with no repeats to perform invariant analysis . My data looks something similar format probename sample1 sample2 sample3 A 2.3 2.4 2.5 A

Thank you. To correct myself, I can indeed reproduce this with R --vanilla too. A reproducible example is: $ R --vanilla R version 3.6.0 Patched (2019-05-31 r76629) -- "Planting of a Tree" ... > Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "true") > loadNamespace("oligo") Error in omittedSig && (signature[omittedSig] != "missing") :

[Perhaps someone could rename this list to dtrace-matt-problems-discuss?] If I run this script against my binary (which contains a USDT probe called ''concurrentq-latency''): ::: / probename == "concurrentq-latency" / { printf("[%s]:[%s]:[%s]\n", probeprov, probefunc, probename); } I get this output: dtrace: script ''testq.d'' matched 46056

**Maybe this bug needs to be understood further before applying the patch because patch is most likely also wrong** Because, from just looking at the expressions, I think neither the R 3.6.0 version: omittedSig <- omittedSig && (signature[omittedSig] != "missing") nor the patched version (I proposed): omittedSig <- omittedSig & (signature[omittedSig] !=

Dear all, I've noticed by trying to download gz files from here : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 At the bottom one can download GSM907811.CEL.gz . If I download this manually and try oligo::read.celfiles("GSM907811.CEL.gz") everything works fine. (oligo is a bioConductor package) However, if I download using download.file("

Henrik, If a minimal reprex is hard to construct, could you perhaps instrument your version of R to include a browser() call at the start of the else if(!all(signature[omittedSig] == "missing")) { branch, run the code that triggers the issue for you (and must hit that branch) and tell us what the "signature" and "omittedSig" objects look like at that point?

Using: untrace(methods::conformMethod) at <- c(12,4,3,2) str(body(methods::conformMethod)[[at]]) ## language omittedSig <- omittedSig && (signature[omittedSig] != "missing") cc <- 0L trace(methods::conformMethod, tracer = quote({ cc <<- cc + 1L print(cc) if (cc == 31) { ## manually identified untrace(methods::conformMethod)

>>>>> Henrik Bengtsson via R-core >>>>> on Sun, 23 Jun 2019 11:29:58 -0700 writes: > Thank you. > To correct myself, I can indeed reproduce this with R --vanilla too. > A reproducible example is: > $ R --vanilla > R version 3.6.0 Patched (2019-05-31 r76629) -- "Planting of a Tree" > ... >>

DISCLAIMER: I can not get this error with R --vanilla, so it only occurs when some other package is also loaded. I don't have time to find to narrow that down for a reproducible example, but I believe the following error in R 3.6.0: > Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "true") > library(oligo) Error in omittedSig && (signature[omittedSig] !=

Hi, I have a list of IPI gene IDs. I want to find out whether there is a package which can map the gene ontology to these IPIs, and plot the pie chart to demonstrate the molecular function distributions. The input is like the following gene IPI IDs: IPI:IPI00008860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q542Y2|ENSEMBL:ENSP00000231338;EN

Argh! Yes you are right, the "fix" doesn't. And I fell into the same "hey it's a vector so && has to be wrong"-trap. So this has to be reverted to something that has at least failed unconspicuously for a decade.... Will do. Thanks to Martin for remaining suspicious! [This code was originally from 2009, by John Chambers. It is not too likely that he'll

>>>>> peter dalgaard >>>>> on Thu, 27 Jun 2019 16:23:14 +0200 writes: > Henrik, > If a minimal reprex is hard to construct, could you perhaps instrument your version of R to include a browser() call at the start of the > else if(!all(signature[omittedSig] == "missing")) { > branch, run the code that triggers the issue

Hello, this is probably something silly which I am doing, but I cannot understand why this allocation is not happening. Here is a my C code which tries to allocate a list of size 333559, and then a matrix of size 8*333559 I thought I might be running into memory problems, but R is not even using that much (I start R with more memory and it stays constant) Also, I start R as I normally do and I

> On 28 Jun 2019, at 16:03 , Martin Maechler <maechler at stat.math.ethz.ch> wrote: > >>>>>> Henrik Bengtsson >>>>>> on Thu, 27 Jun 2019 16:00:39 -0700 writes: > >> Using: >> >> untrace(methods::conformMethod) >> at <- c(12,4,3,2) >> str(body(methods::conformMethod)[[at]]) >> ## language omittedSig

>>>>> Henrik Bengtsson >>>>> on Thu, 27 Jun 2019 16:00:39 -0700 writes: > Using: > > untrace(methods::conformMethod) > at <- c(12,4,3,2) > str(body(methods::conformMethod)[[at]]) > ## language omittedSig <- omittedSig && (signature[omittedSig] != "missing") > cc <- 0L > trace(methods::conformMethod, tracer =

On 05/02/2018 03:21 PM, Joris Meys wrote: > Dear all, > > I've noticed by trying to download gz files from here : > https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 > > At the bottom one can download GSM907811.CEL.gz . If I download this > manually and try > > oligo::read.celfiles("GSM907811.CEL.gz") > > everything works fine. (oligo