Sharpening Image
Calculating foregound
Error in BLData at ProbeID[, i] <- dat1$ProbeID[ord]
number of items to replace is not a multiple of replacement
length
>
#-------------------------------------------------------------------
Reading bead summary data:
#-------------------------------------------------------------------
targets<-readBeadSummaryTargets...targets)…
Order by: Relevance
04/29/04
03:47PM >>>
Dear Bioconductor users,
I am currently running the latest version of affy 1.4.22 under
R 1.9.0 on Mac OSX 10.3. I am able to get a boxplot on the
unnormalized
data
but not on the normalized...howard1.raw
AffyBatch object
size of arrays=640x640 features (67206 kb)
cdf=MG_U74Av2 (12488 affyids)
number of samples=21
number of genes=12488
annotatio…
updated 21.6 years ago • James W. MacDonald
hgnc_symbol"),filters="affy_hg_
u95av2",values=c("1939_at"), mart=human.ensembl,verbose=TRUE)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query>
<query count="0" datasetconfigversion="0.6" requestid="biomaRt" uniquerows="1" virtualschemaname...filters = "affy_hg_u95av2", :
The query to the BioMart webservice returned an invalid result: the
number of columns in the result tabl…
1.4 on a
solaris8/sun4u system building with gcc 3.4.0 and I'm having problems
with the release version (1.2.2) of RBGL. (I've been able to get all
other packages loaded).
First is the previously reported issue with the z option...of tar, but
even with that fixed, I get the errors below.
Versions 1.2.5 and the latest 1.3.7 work (or at least install fine),
but
as has been pointed out many times,…
div class="preformatted">This should be fixed now int the latest devel version 1.1.15. I did
find a
related bug that prevented connecting lines of grouped track items to
be
plotted when zoomed...wtimp1 at="" jhmi.edu=""> wrote:
>
>>I have run into a different problem with the devel version of Gviz:
>>
>>If I try to plot a GeneRegionTrack deri…
updated 13.3 years ago • florian.hahne@novartis.com
there is a function for the GOHyperGResult object
(geneIdUniverse)
which retrieves the entrez gene identifiers from your gene universe
for all the
tested GO terms. Is there a way to get only the entrez gene
identifiers from...the p-value cutoff? Is there a function which could be
applied to
this list to change those entrez identifiers into gene names? Or is
there an
easier way to get the names…
We frequently analyze our gene expression data using WGCNA to identify modules of gene co-expression profiles. However, in generating our original dendrograms we obtain blocks that...We frequently analyze our gene expression data using WGCNA to identify modules of gene co-expression profiles. However, in generating our original dendrograms we obtain blocks that have...of 0.9 was selected (blue da…
updated 8.7 years ago • ngeraci
you for advance for your answer and your help.
------------------------------
My Session Info:
R version 2.15.1 (2012-06-22)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF...Office Address: Angel Building, 407 St John Street, London
EC1V 4AD.
[[alternative HTML version deleted]]
</sophie.lamarre@insa-toulouse.fr>…
interested in understanding how mutations in cancer alter molecular interaction networks and in identifying ways to target these alterations therapeutically. We have a particular interest in identifying and understanding
updated 2.8 years ago • Colm
Hello,
apologies, I am confused by the following. It seems that people often use Deseq2 to identify differential amplitude of gene expression, but dexseq to identify alternative splicing.
However, Deseq2 can
<div class="preformatted">While testing ArrayExpress with E-GEOD-17215 I see
Error in rma(ae) :
VECTOR_ELT() can only be applied to a 'list', not a 'character'
being thrown by rma applied to the downloaded AffyBatch - shown below.
Not
sure whether this is a problem with the source data at ArrayExpress or
stupidity on my own part, but I can't find any sign of this specific
error
text in an…
updated 16.2 years ago • Ross Lazarus
my R to 2.15.2 and reloaded the bioc packages. Then
I
started to have troubles making use of a number of packages, not the
least
with OLIGO which I have been using frequently before this updating.
Can
someone in the know...R/2.15/library/bit/libs/x86_64/bit.so,
6):
Library not loaded:
/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib
Referenced from:
/Users/yb8d/Library/R/2…
Error in open.connection(x, "rb") : HTTP error 403.
```
This happens for every accession number.
When i garbage collect with `gc()` i get:
```
> Warning messages: 1: In .Internal(gc(verbose, reset, full)) :
> closing unused connection...a lot of series and so wanted to use getGEO's ability to pull this information with just accession numbers.
Thanks in advance!
```
…
updated 6.6 years ago • andy_shaps
Dear all,
I ran into the following problem: for some reason one sequence (Accession number: MN603925.1) does not seem to align properly, using the DECIPHER package.
As shown in the image, the entire sequence ought...Max
```r
setwd("<
<working directory="">>")
#I download the following 3 accession numbers (i.e. FASTA files; gene: 23s) from GENBANK nucleotide to m…
contrast.matrix)
fit2<-eBayes(fit2)
write.table(topTable(fit2, coef=1, adjust="fdr", sort.by="B",
number=50000),
file="limmadn_wt.xls", row.names=F, sep="\t")
write.table(topTable(fit2, coef=2, adjust="fdr", sort.by="B",
number=50000),
file...limmaestw_wt.xls", row.names=F, sep="\t")
[[alternative HTML version deleted]]
</div
and they are. The MM
index
always is 732 greater than its corresponding PM index).
Also, the number of indices returned by the pmindex, mmindex and
probeIndex functions is 42 less than the number of probes in the
drosophila2probe...darwin7.4.0
status
major 1
minor 9.1
year 2004
month 06
day 21
language R
affy version 1.4.32
Thanks very much for your help,
Eric
--
Dr. Eric Bl…
updated 20.3 years ago • Eric Blanc
in bioconductor. On the
http://www.bioconductor.org/data/cdfenvs/cdfenvs.html site, there are
a
number of CDF files for E.coli that can be downloaded. The problem is
that
there is no such file for the E.coli antisense chip...ecoliasv2" and "ecoli" chip (please refer to the URL).
I
was wondering if these chips are different versions to the one I am
using,
in which case I can probably use them .
…
<div class="preformatted">Dear list,
I'm using heatmap.2 to construct heatmap of my array results.
>heatmap.2(x,col=redgreen(75), scale="row", key=TRUE, symkey=FALSE,
density.info="none", trace="none", cexRow=0.5, cexCol=0.9,
margins=c(5,5),
keysize=1.5)
Since I have around 100 data on the heatmap, the ID numbers for are
hard to
see on the map. How can I make the heatmap bigger so t…
updated 16.5 years ago • Wei Xu
gt; image(data[,1]);
Warning message:
data length [22690] is not a sub-multiple or multiple of the number of
rows [712] in matrix
The resulting image shows diagonal lines that shouldn't be there.
Could anyone put me on the right...track?
Thanks for your help.
Joel Malard
[[alternative HTML version deleted]]</div
updated 20.5 years ago • Malard, Joel M
Hi,
I have some question regarding the ‘paired’ argument and how to use it in MeDIPS (version 1.23.2)
1. If ‘paired’ = true, are the arguments ‘extend’ and ‘shift’ then ignored automatically?
2. If ‘paired’ = true, how does normalization...files are created: in my data I have reads of 49 bp. I set the ‘window\_size’ = 50. Is it then the numbers of reads (49 bp) or also fragments (around 200…
updated 9.2 years ago • stb
div class="preformatted">Hello all,
I am working with data with a very large number of differentially
expressed
genes (liver cancer samples), and wish to demonstrate for my advisor
and
committee the...Mikki Behnke
Integrative Life Sciences
Virginia Commonwealth University
[[alternative HTML version deleted]]
</div
div class="preformatted">Hi,
We have 4 cases and 5 controls. We would like to add RIN number as one
of the covariates to the data analysis. Here is my code which gives
errors:
> countsTable=read.table("4Cases_5Controls_counts.txt...NIMH/NIH
Blg 35, Rm 1A/205
Bethesda, MD - 20892
Phone# 301-451-4258
[[alternative HTML version deleted]]
</div
<div class="preformatted">Dear Mark, Gordon,
probably a naive statistical question on edgeR : considering 3
samples of
3 library sizes : a) 10 mil reads, b) 30 mil reads, and c) 12 mil
reads.
after applying edgeR, I do obtain 1) > 2000 genes differentially
expressed
between a) and b) (FDR< 0.01, FC > 2), and 2) only ~ 200 genes
differentially expressed between a) and…
PACKAGE =
"affy") :
C entry point "ReadHeader" not in DLL for package "affy"
Enter a frame number, or 0 to exit
1: justRMA()
2: just.rma(filenames = l$filenames, phenoData = l$phenoData,
description = l$
Selection: c
Enter an item...from the menu, or 0 to exit
Selection: 0
> sessionInfo()
Version 2.3.0 Under development (unstable) (2006-03-12 r37524)
i386-pc-mingw32
attached ba…
packages and ended up making
a package, AnnotationFuncs, for it. It handles mapping from one
identifier to another (via the central identifier), using the data
packages. I have included an example below.
> library(AnnotationFuncs...shed some light on the following.
Given a set of gene symbols I would like to retrieve different
identifiers.
Using the org.Xx.eg.db packages I can go about …
updated 14.2 years ago • Stefan McKinnon Høj-Edwards
messages:
1: Use BiocIO::FileForFormat
2: Use BiocIO::FileForFormat
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath...version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
Warning in readGFF(filepath...version = version, filter …
updated 3.4 years ago • bonob
Bioconductor packages 'beadarray' and 'BeadExplorer', it
looks like these accommodate Beadstudio version 1 and 2 data, while
our
data was created by BeadStudio version 3.0.14.. Would it still work?
My
collaborator sent two types...of files to me: (1) a number of .csv files
(read by excel, 2 for each sample) with columns Illumicode, N, mean
GRN,
Dev GRN. (2) a summary .txt file with columns
<div class="preformatted">Dear list,
It turned out the slowness and out of memory has nothing to do with
bioconductor package.
I tested it by the following:
test.intensity <- test@exprs #where test.intensity is a 0.5 miliion x
5
matrix
plot(data.frame(test.intenisty)) # scatter plot for replicate
comparison.
it took >10 mins after I increased the memory size. (I was runni…
<div class="preformatted">Dear all,
I got the following error message when I was trying to use the
function âgetCrlmmSummaries()â to retrieve results generated by
running CRLMM genotyping algorithm successfully over 9 Affy SNP 6.0
chips.
####################
> outObj_crlmm<-getCrlmmSummaries(outDir)
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal…
4090550
I can use the following code to obtain a single sequence by typing in
the chromosome number, start and stop manually:
> library(BSgenome.Mmusculus.UCSC.mm9)
> seq1 = subseq(Mmusculus$chr9,79466420,79466570...at a time. Please find below the sessionInfo.
Thank you for any help,
Simon
> sessionInfo()
R version 2.8.1 (2008-12-22)
i386-pc-mingw32
locale:
LC_COLLATE…
I have a list of transcript IDs from affymetrix Rat Exon arrays.
I would like to get some associated identifiers such as the entrez
gene id or th gene symbol.
I have done the following
######################
library("biomaRt")
### Seleccio de la base de dades...alternative HTML version deleted]]
</div
how can I annotate these 292681 values with the correct probenames or fid's (means: feature identifier?).
--- SESSION INFO ---
<pre>
R version 3.2.2 (2015-08-14)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific
updated 9.9 years ago • dietmar.pils
<div class="preformatted">Dear Colleagues,
Please excuse this email if you have received it more than once.
I am writing to let you know that we are chairing a special section on
Alternative Splicing for PSB 2004 (Pacific Symposium on Biocomputing
2004).
This meeting will be held Jan. 6-10, 2004 at the Fairmont Orchid in
Kona on
the big island of Hawaii.
For this session, we will focus o…
48 01
t48_r2 48 02
t48_r3 48 03
```
The main objective of the study is to identify genes that are expressed in a circadian manner. I have decided that I will use [`MetaCycle`][1] to identify the "circadian...For instance, would it make any sense to perform an all-vs.-all differential expression analysis and identify significantly expressed genes shared between all pairw…
updated 2.9 years ago • Dunois
to factors
## Note: levels of factors in the design contain characters other than
## letters, numbers, '_' and '.'. It is recommended (but not required) to use
## only letters, numbers, and delimiters '_' or '.', as these are safe characters...dds <- dds[keep,]
dds # n= 24,038
## class: DESeqDataSet
## dim: 24038 13
## metadata(1): version
## assays(1): counts
## rownames(24038): E…
updated 3.7 years ago • Manav
external tools.
To use the full potential of openPrimeR, please make sure
that the required versions of the speciied tools are
installed and that they are functional:
o MELTING (http://www.ebi.ac.uk/biomodels/tools...melting/)
The number of cores for was set to '2' by 'parallel_setup()'.
sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit...RCurl_…
updated 4.4 years ago • benedikt.kirchner
start(solved_SEW),
width(solved_SEW), :
negative length vectors are not allowed
Enter a frame number, or 0 to exit
1: DNAStringSet(myseq)
2: XStringSet("DNA", x, start = start, end = end, width = width,
use.names
= u
3: XStringSet("DNA", x, start...Somehow there must be an overflow ... .
Here's some more info on my system:
> sessionInfo()
R version 2.11.1 Patched (2010-06-20 r52342…
40 samples that are split into 4 groups and are treated in
one of 2 ways.
What I want to do is identify genes with an interaction effect between
group and treatment.
What would the best way to go about this? I have attempted...1]) == 1 | abs(interDTest[,2]) == 1 |
abs(interDTest[,3]) == 1)
Is this a suitable way to identify the genes with an interaction
effect?
So far, from looking at expression…
updated 17.8 years ago • Sebastien Gerega
Hello,
I'm working on a transcriptome sequencing dataset (not RNA-seq but QuantSeq libraries, but that's not important for this question) and I am (among other things) interested in differential gene expression analysis. I already use edgeR and DESeq2 and would add limma soon. Now I wonder whether I can use these tools to validate the identified genes?
Of course I need wet lab validation to som…
<div class="preformatted">Hi there,
I was having some trouble using rtracklayer to obtain phyloP scores -
I think maybe I have found a problem with rtracklayer. Is there a
limit to the number of scores/positions it can get in a single query?
Hopefully the code and output below will explain all. I am using the
devel...phyloP scores -
I think maybe I have found a problem with rtracklayer. I…
updated 12.4 years ago • Janet Young
the
BH method gets the adjusted p-value (alpha) from [P_k*n*c(n) ] / k <
alpha,
where n = total number of genes (tests), P_k = p-value at kth gene
(genes
ordered from low to high p-value), and k = number of genes with
p-value less
than...who can point me in the right direction. Thanks in advance,
Dave Young
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i386-pc-mingw32/i…
updated 14.2 years ago • David Young
Biobase")' and for packages 'citation(pkgname)'.
Warning message:
package 'affy' was built under R version 2.9.1
> affy.data <- ReadAffy()
> affy.data
AffyBatch object
size of arrays=712x712 features (11 kb)
cdf=ATH1-121501...22810 affyids)
number of samples=24
number of genes=22810
annotation=ath1121501
notes=
>
> prefix <- "Guido"
>
> #ge…
updated 15.8 years ago • Guido Hooiveld
<div class="preformatted">Hi all,
I'm picking up on an older thread
(https://stat.ethz.ch/pipermail/bioconductor/2006-August/013881.html
) which poses the following question: What are the most appropriate
methods for normalization in the face of large numbers of
differentially expressed genes? Aside from this 2006 thread, I've
found only one publication on the topic (http://www.ncbi.…
updated 16.5 years ago • David Garfield
I downloaded the newest version of R as I kept getting prompted to update in RStudio. As I did, for some reason, previous work I had done following the...I downloaded the newest version of R as I kept getting prompted to update in RStudio. As I did, for some reason, previous work I had done following the DESeq2
updated 2.5 years ago • saguiar
Hello,
Both the GSVA module's implementation of ssGSEA and the Broad/GenePattern implementation ([https://github.com/broadinstitute/ssGSEA2.0][1]) are based on the papers from Barbie et al (1) and Abazeed et al (2), however, I cannot find a combination of parameters for which they produce identical results to each other.
For example, taking the random matrices a la the GSVA documentation:
```r…
updated 14 months ago • Bob
to look at all other genes.
Here is my cuestion. I get very different LogFC depending on DESeq version, and I'm therefore in doubt which one I should use, also when taking into acount that I would like the LogFC of these 5...nbsp; 9.998854e-01
Otud7a 1.639533e-94
Chrna7 9.713749e-18
sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86\_64-unknown-linux-g…
updated 10.9 years ago • madal
when
I tried to continue the analysis using snapCGH package. Please find
below my session info:
R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64...data format for CNA object has been
postponed
in order to ensure backward compatibility with older versions of
DNAcopy
****************************************************…
2
4 O88737 2
5 P06837 2
6 P0C7M9 2
string_db <- STRINGdb$new(version="10",species=10090,score_threshold=400, input_directory="" )mapped <- string_db$map( list_wttg, "list_wttg", removeUnmappedRows...on the browser "string-db.org/10/p/9425227685" I get redirected to this page:
http://string-db.org/version\_10/newstring\_cgi/go.pl?id=9425227685
that is tel…
updated 8.6 years ago • Ilario De Toma
<div class="preformatted">Hi David,
I was trying the package to get at the genes for each node, and tried
the code you suggested. However, for some nodes/pathways, they seem to
give an error. For example:
##----------
library(KEGGgraph)
# Glycolysis pathway
xfile <- system.file("/extdata/hsa00010.xml", package="KEGGgraph")
p <- parseKGML(xfile)
## -------------…
of running can be seen from below. Thanks a lot!
Weiwei
> biocLite("GEOquery")
Running getBioC version 0.1.8 with R version 2.3.1
Running biocinstall version 1.8.5 with R version 2.3.1
Your version of R requires version...The downloaded packages are in
/tmp/RtmpnbgyQZ/downloaded_packages
Warning messages:
1: number of rows of result
is not a multiple of vector length (arg…
I am currently in the process importing Kallisto data for a mouse RNAseq experiment using the ```tximport``` package and am creating ```tx2gene``` objects to use for mapping. I decided to try three different annotation packages: (1) ```org.Mm.eg.db```, (2) ```EnsDb.Mmusculus.v79```, and (3) ```biomaRt```. However, when I ran the code (shown below) to extract the transcript to gene mappings, I on…
updated 11 months ago • Nicholas
in : Test.CEL
Error in data.frame(exprs = filenames, dates = dates) :
arguments imply differing number of rows: 1, 0
I tried the previous version of oligo (1.26.6), and it seems to work
just
fine. But the latest version (1.28.0) is...m
seeing
the same behavior on two different computers. Below is the session
info
for one of them.
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu…
works as expected. My </span>mzIdentML data was exported using Scaffold 4.4.5 (linux version).
<pre>
> library(mzR)
Loading required package: Rcpp
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple...openIDfile("150602Nakai_mus.mzid.gz")
> x
Identification file handle.
Filename: foo.mzid.gz
Number of psms: 1150
&…
updated 10.4 years ago • Diego Diez
What does the 'coef' argument to topTable() actually do?
I know it says in the manual:
column number or column name specifying which coefficient or
contrast of the linear model is of interest
But what does that mean...coef=2), I get an
error.
Which of those isn't a coefficient and why not?
[[alternative HTML version deleted]]
</div
updated 12.5 years ago • Ed Siefker
Sciences
University of Montana
Missoula, Montana 59812-4824
Office Telephone: (406) 243-4977
Fax Number: (406) 243-4184
E-mail: Mark.Grimes@mso.umt.edu
[[alternative HTML version deleted]]
</div
updated 12.7 years ago • Grimes Mark
the maploc argument
is
"the locations of marker on the genome. Vector of length same as the
number
of rows of genomdat. This has to be numeric." So it has to be numeric
from
the DNAcopy documentation. Is it the first value...I cant seem to find any clarification on
this
anywhere.
Nikolas Balanis
[[alternative HTML version deleted]]
</div
data structures and methods for
representing and computing on graphs (collections of nodes and edges).
Version 1.10.0, available in the Bioc 1.8 release (requires R 2.3.0)
includes a number enhancements as described below.
* Node
DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/mvtnorm/libs/mvtnorm.so':
\`maximal number of DLLs reached...
In addition: Warning messages
updated 7.7 years ago • doctorjiangtao
I am trying to get a VCF stack from the 1000 genome project using package "ldblock" on R (version 4.0.3), but when I used function
```r
sta = stack1kg()
```
the following error was shown.
Error in open.BcfFile(BcfFile(file, character...I tried stack1kg(chrs = as.character(1:22)) and manually change the number from 1 to 22, all shown similar message as above (the only thing that changed …
updated 4.8 years ago • ting835698
You have an error in
your SQL syntax; check the manual that corresponds to your MySQL
server
version for the right syntax to use near '[i] where geni like
geni_FClow$geni[i]' at line 1)/
while the simple statement:
/dbGetQuery...set FC_low =
geni_FClow$FC_low[2] where geni like geni_FClow$geni[2]")/
(using a number instead of the [i])
works!
Any help would be appreciated
(I know maybe the ans…
updated 18.5 years ago • Alessandro Bruselles
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
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Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
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BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
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Michael Love
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The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup.
Maybe give the traceb…
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