similar to: download.file does not process gz files correctly (truncates them?)

Dear all, I've been diving a bit deeper into this per request of Tomas Kalibra, and found the following : - the lock on the file is only after trying to read it using oligo, so that's not a R problem in itself. The problem is independent of extrenal packages. - using Windows' fc utility and cygwin's cmp utility I found out that every so often the download.file() function inserts

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

Use mode="wb" when you download the file. See https://github.com/HenrikBengtsson/Wishlist-for-R/issues/30. R core, and others, is there a good argument for why we are not making this the default download mode? It seems like a such a simple fix to such a common "mistake". Henrik On Thu, May 3, 2018, 00:44 Joris Meys <jorismeys at gmail.com> wrote: > Dear all, >

Using the correct mode absolutely solves it. Apologies for not trying the obvious. Cheers Joris On Thu, May 3, 2018 at 2:10 PM, Martin Morgan <martin.morgan at roswellpark.org > wrote: > > > On 05/02/2018 03:21 PM, Joris Meys wrote: > >> Dear all, >> >> I've noticed by trying to download gz files from here : >>

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>

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

Hi all! While I am trying to read .cel files with oligo package: afbatch=read.celfiles(list.celfiles()) I get an error: Package 'pd.mirna.1.0.2xgain' was not found in the BioConductor repository How can I overcome this? Thank you in advance

I think that you misunderstood me. As far as I know, RMA does three things: background correction, quantile normalization, and summary from probes to probesets. I want the probe values after background correction and quantile normalization but before the summary. On Sat, Dec 26, 2009 at 12:07 PM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote: > pm(data) > > b > > On Dec

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") :

**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] !=

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?

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] !=

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)

> 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

Hello, I have a data frame consisting of four columns and would like to sort based on the first column and then write the sorted data frame to a file. > df <- read.table("file.txt", sep="\t") where file.txt is simply a tab-delimited file containing 4 columns of data (first 2 numeric, second 2 character). I then do, > df_ordered <- df[order(df$V1), ] OR,

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

Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best

Dear Sirs/Madam, I am a beginner to R, and I am currently working on a data matrix which looks like this: > head(oligo) ko:K00001 ko:K00003 ko:K00005 ko:K00008 ko:K00009 ko:K00010 ko:K00012 AAA 370 631 365 67 164 455 491 KAA 603 1208 170 157 68

I'm having trouble getting summaries out of the 250K snp chips in R. I'm using the oligo package and when I attempt to create the necessary SnpQSet object (to get genotype calls and intensities) using snprma, I encounter memory issues. Anyone have an alternative package or workaround for these large snp chips? -- View this message in context:

Hi, ExonFeatureSet I have an object of the above class. The following document mentioned it. http://www.bioconductor.org/packages/2.5/bioc/vignettes/oligo/inst/doc/ClassesUsedInOligo.pdf But I would like to see its defintion. I'm wondering if there is a way in R to give me the definition of any class? Regards, Peng