Displaying 20 results from an estimated 47 matches for "oligos".
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oligo
2012 Oct 07
1
BioConductor package: '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>
2019 Jun 23
2
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
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") :
2019 Jun 25
3
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
**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] !=
2008 May 19
1
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:
2008 May 19
0
[BioC] oligo ids
Thanks Sean!
Your reply was very helpful. I already got almost what I wanted. I have some
NA values but I will look if I can find them through bibliography 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,
2018 May 02
7
download.file does not process gz files correctly (truncates them?)
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("
2019 Jun 27
2
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
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?
2019 Jun 27
2
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
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)
2019 Jun 24
0
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
>>>>> 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"
> ...
>>
2019 Jun 25
0
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
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
2019 Jun 22
2
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
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] !=
2005 Jul 12
1
allocation of large matrix failing
...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 ever...
2019 Jun 27
0
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
>>>>> 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
2019 Jun 28
2
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
> 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
2009 Jan 27
1
Problem with RMA using limma, oligo and pdInfoBuilder packages
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
2019 Jun 28
0
methods package: A _R_CHECK_LENGTH_1_LOGIC2_=true error
>>>>> 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 =
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
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
2018 May 03
0
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
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
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,
>
2018 May 03
0
download.file does not process gz files correctly (truncates them?)
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 :
>>