search for: oligo

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> <DNAStringSet> > 1 990...

...k 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") : 'length(x) = 4 > 1' in coercion to 'logical(1)' Error: unable to load R code in package ?oligo? /Henrik On Sun, Jun 23, 2019 at 1:54 AM peter dalgaard <pdalgd at gmail.com> wrote: &gt...

...laimer: Please note that I have not at all studied the rest of the function, so the above is just based on that single line plus debugging that 'omittedSig' is a logical vector. Martin, I don't have the time to dive into this further. Though I did try to see if it happened when one of oligo's dependencies were loaded, but that was not the case. It kicks in when oligo is loaded. FYI, I can also replicate your non-replicatation on another R 3.6.0 version. I'll see if I can narrow down what's different, e.g. comparing sessionInfo():s, etc. However, I want to reply with findi...

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 probe...

...iography or an external tool. Best Regards, Eleni On Mon, May 19, 2008 at 6:07 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Mon, May 19, 2008 at 10:47 AM, Eleni Christodoulou > <elenichri@gmail.com> wrote: > > 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 id...

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(" https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz ", destfile = "GS...

...udied the rest of the >> function, so the above is just based on that single line plus >> debugging that 'omittedSig' is a logical vector. >> >> Martin, I don't have the time to dive into this further. Though I did >> try to see if it happened when one of oligo's dependencies were >> loaded, but that was not the case. It kicks in when oligo is loaded. >> FYI, I can also replicate your non-replicatation on another R 3.6.0 >> version. I'll see if I can narrow down what's different, e.g. >> comparing sessionInfo():s, etc....

...d untrace(methods::conformMethod) trace(methods::conformMethod, at = list(at), tracer = quote({ str(list(signature = signature, mnames = mnames, fnames = fnames)) print(ls()) try(str(list(omittedSig = omittedSig, signature = signature))) })) } })) loadNamespace("oligo") gives: Untracing function "conformMethod" in package "methods" Tracing function "conformMethod" in package "methods" Tracing conformMethod(signature, mnames, fnames, f, fdef, definition) step 12,4,3,2 List of 3 $ signature: Named chr [1:4] "Til...

...is 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") : > 'length(x) = 4 > 1' in coercion to 'logical(1)' > Error: unable to load R code in package ?oligo? > /Henrik Thank you Henrik, for the report, etc, but hmm... a...

...I have not at all studied the rest of the > function, so the above is just based on that single line plus > debugging that 'omittedSig' is a logical vector. > > Martin, I don't have the time to dive into this further. Though I did > try to see if it happened when one of oligo's dependencies were > loaded, but that was not the case. It kicks in when oligo is loaded. > FYI, I can also replicate your non-replicatation on another R 3.6.0 > version. I'll see if I can narrow down what's different, e.g. > comparing sessionInfo():s, etc. However, I want...

...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] != "missing") : 'length(x) = 4 > 1' in coercion to 'logical(1)' Error: unable to load R code in package 'oligo' is because of a '_R_CHECK_LENGTH_1_LOGIC2_=true' mistake in the 'methods' pa...

...y do and I allocate a matrix of that size and it returns instantly, so I am inclined to think that this is not a memory/GC issue, but I submit it may be. <code> int numHits = seq.GetNumberHits(); Rprintf("numHits:%d\n", numHits); Rprintf("before allocation...\n"); SEXP oligos, matrix; PROTECT(oligos = NEW_LIST(numHits)); Rprintf("allocated oligo list...\n"); PROTECT(matrix = NEW_INTEGER(numHits*8)); Rprintf("entering looop...\n"); <output> entering sequence loop. numHits:333559 before allocation... allocated oligo list... It hangs here eve...

...unction, so the above is just based on that single line plus >>> debugging that 'omittedSig' is a logical vector. >>> >>> Martin, I don't have the time to dive into this further. Though I did >>> try to see if it happened when one of oligo's dependencies were >>> loaded, but that was not the case. It kicks in when oligo is loaded. >>> FYI, I can also replicate your non-replicatation on another R 3.6.0 >>> version. I'll see if I can narrow down what's different, e.g. >>>...

...onformMethod, at = list(at), tracer = quote({ >> str(list(signature = signature, mnames = mnames, fnames = fnames)) >> print(ls()) >> try(str(list(omittedSig = omittedSig, signature = signature))) >> })) >> } >> })) >> loadNamespace("oligo") >> >> gives: >> >> Untracing function "conformMethod" in package "methods" >> Tracing function "conformMethod" in package "methods" >> Tracing conformMethod(signature, mnames, fnames, f, fdef, definition) >>...

...ges. 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 of the questions and responses on this mailing list, I decided to use pdInfoBuilder, oligo and limma packages to run analysis. The problem is, at the end, I get expression and differential expression measured for all probe separately but not the calculated expression representing all probe of each gene. When I run RMA, I got only two steps, Background correcting and Normalizing but not C...

...t; trace(methods::conformMethod, at = list(at), tracer = quote({ > str(list(signature = signature, mnames = mnames, fnames = fnames)) > print(ls()) > try(str(list(omittedSig = omittedSig, signature = signature))) > })) > } > })) > loadNamespace("oligo") > > gives: > > Untracing function "conformMethod" in package "methods" > Tracing function "conformMethod" in package "methods" > Tracing conformMethod(signature, mnames, fnames, f, fdef, definition) > step 12,4,3,2 > List of 3...

...2/2018 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 is a bioConductor package) > > However, if I download using > > download.file(" > https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz > &...

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 an extra byte. There's no real obvious pattern in how these bytes are add...

...lt;jorismeys at gmail.com> 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 is a bioConductor package) > > However, if I download using > > download.file(" > > https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&format=file&file=GSM907811%2ECEL%2Egz >...

...; >> 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(" >> https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907811&for >> mat=file&a...