Hi CNAnorm users
I am using CNAnorm for identifying somatic CNV's from shallow WGS of FFPE samples. I have access to the tumor and the paired control samples. I have...CN, exclude=toSkip, method="density") \# I used density method to get integer copy number levels from sample
plotPeaks(CN)
CN <- validation(CN)
seg\_list <- list(a…
Order by: Relevance
genome coordinate annotated in repeat masker, as well as the canonical sequence of the repeats the identify reads that belongs to different repeat classes.
[Sample output format of repenrich2][1]
All samples(both IP and input...has the same number of total read count.
During this process, I found that the input of mutant cells has a lot more reads with the annotation
updated 5.7 years ago • mkmwong
me with two
problems, first I'm not sure I can get the pattern matching working
well enough to identify which entry numbers in the cdf file correspond
to the gene list I have, and secondly, people have already commented
the 12-condition experiment is replicated
3
times. One thing I'd like to do with this dataset is to identify a set
of "housekeeping" genes specific to this data, i.e. genes whose levels
do not change very much across all the samples...Is there a good way to
get a single number for each gene that represents its level of
variability? Should I just estimate per-gene dispersions with edgeR
using
I am using EdgeR to find DE genes in my data. In order to reduce necessary sequencing depth, I have been enriching my sequencing libraries for 300 genes of interest before sequencing (described here: http://www.ncbi.nlm.nih.gov/pubmed/24705597) and then running EdgeR DE analysis on only those genes. I am comparing gene expression between two experimental conditions.
I have been getting …
updated 9.3 years ago • tyssowski
Hello,
Can you please suggest R packages for analyzing affy SNP 6 and 250K as
well as copy number variations for sequencing data? Thanks.
John
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updated 14.2 years ago • John linux-user
div class="preformatted">Only a small number of seats remain for the boston course.
For information see https://secure.bioconductor.org/BostonFeb09/
blog at bosbioc.wordpress.com...has some additional discussion
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updated 16.9 years ago • Vincent J. Carey, Jr.
Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
compa
ny registered in England with number 2742969, whose registered
office is 2
15 Euston Road, London...NW1 2BE.
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updated 14.5 years ago • Salih Tuna
<div class="preformatted">Hi,
I am trying to use Gviz to retrieve info from specific regions on the
genome using the BiomartGeneRegionTrack function. This goes fine with
all
chromosomes except X (and possibly Y, have not been able to test
that).
When I retrieve data for an empty region (20000-30000) all goes fine,
but
in a region with genes (17740000-17750000) the following error occurs:
…
updated 12.5 years ago • Martin Rijlaarsdam
is `AS_SB_TABLE=1067,529|5,196`. However, `readVcf` seems to split by `,` and take only the first number (1067) - this is what I see in R:
```
> m2crct = readVcf('somatic_mutect2.filtered.vcf.gz')
> head(info(m2crct)$AS_SB_TABLE...not in GATK - in the field description it is stated that it should be a String and have one element (Number=1). So it should not be split by `,`. Comma…
updated 2.9 years ago • gennady.margolin
PC that had a fresh install of R 2.4.1 and everything else
in
March 2007, so I know it's not my R version.
Thanks,
Jenny
> coef6 <- topTable(fit2,coef=6,number=100,resort.by="P")
#works fine
> coef6 <- topTable(fit2,coef=6,number...100,resort.by="A")
#works fine
> coef6 <- topTable(fit2,coef=6,number=100,sort.by="M") #works fine
> coef6 &a…
SampleNames that
match the CEL files are stored in the first column of Data.
I am using the current version of R and BioC packages, not the devel
versions.
Thanks,
Mark
> ?QCReport
> paste(experiment.designator, "AffyQCReport.pdf...gt; object
AffyBatch object
size of arrays=834x834 features (157603 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=29
number of genes=31099
anno…
these;
3. do hyperGTest(KEGGHyperGParams).
When I try this using the Illumina gene identifiers, I get the following error message:
<pre>
Error in getUniverseHelper(probes, p@datPkg, universeGeneIds(p)) :
After...ID used by your annotation package.
For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).</pre>
…
lt;-ReadAffy()
AffyBatch object
size of arrays=534x534 features (4458 kb)
cdf=RG_U34A (8799 affyids)
number of samples=2
number of genes=8799
annotation=rgu34a
notes=
Warning message:
the condition has length > 1 and only the...correcting...done.
normalizing...[1] "samples= 100 k= 5 first= 0"
Error in rep(data, t1) : invalid number of copies in "rep"
In addition: There were 50 or more warn…
updated 22.6 years ago • Knud Josefsen
<div class="preformatted">Hi,
I'm totally new to the field, I've never used R before, but I need to
normalize some expression data.
In every file I have many columns corresponding to different samples
(different source cells) and rows corresponding to different genes.
However
I have many different files corresponding to different experiments and
they
have different total numbers of rows (…
updated 12.6 years ago • Jan Zaucha
first
step, working on the non-specific filtering by removing probe sets
that have no
Entrez Gene identifier I found the following error:
>entrezIds<-mget(featureNames(eset_sample1), mgug4122aENTREZID)
Error in .checkKeys...value, Lkeys(x), x@ifnotfound) :
value for "A_55_P2045896" not found
>sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386…
on differential expression
analysis of
my smallRNA library deep sequencing data and trying to identify
differentially expressed miRNAs, using edgeR package. I have 24
different
samples with 2 biological replicates...really appreciate any suggestion on this!
Thanks in advance,
Daniela
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updated 13.3 years ago • Danie
<div class="preformatted">Please, do you know whether there exists any mart attributes, for homo
sapiens dataset, that corresponds to what is recorded on miRDB and
called Gene_Bank_Access_Number ?
For example, many such records can be found in file
"MirTarget2_v3.0_prediction_result.txt.gz" downloadable from miRDB
(http://mirdb.org/miRDB/download.html)
In the following I have pasted som…
updated 16.4 years ago • mauede@alice.it
gene level and
exon
level probeset ids for my alternatively spliced exons (then Iwould use
them
to identify the Isoform for the alternative splicing event) as in the
manual
is mentioned.
Everytime I try to use the inspecting...Is there something wrong in what
I do?
Many thank
--
Guido Leoni
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</div
updated 16.5 years ago • Guido Leoni
3) UTR, 4) intergenic. For the first 3 categories,
it would be great if the gene name could also be identified. Can
anybody point me to some function or package? Thanks.
-Kunbin
______________________________________________________________________...and delete this message, along with any
attachments, from your computer.
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mus_musculus/Mus_musculus.GRCm38.99.gtf.gz
But it seems like org.Mm.eg.db is not updating to that version of Mm's ensembl?
tried both
res$symbol <- mapIds(org.Mm.eg.db,
+ keys=ens.str,
+ column="SYMBOL",
+ keytype="ENSEMBL",
+ multiVals
updated 5.7 years ago • kavator
matchprobes. My problem is that
the
resulting AffyBatch object has array sizes of 0x0. I am running
version
2.1.0 of R for windows and have version 1.0.22 of matchprobes.
Here is my code:
pd1<-new("phenoData",pData=data.frame...I get
>comb
$dat
AffyBatch object
size of arrays=0x0 features (523 kb)
cdf=newset (1036 affyids)
number of samples=2
number of genes=1036
annotation=
$c…
updated 20.6 years ago • Jared J. Bisogni
123)
> g1 = randomEGraph(LETTERS[1:15], edges=100)
> g1
A graphNEL graph with undirected edges
Number of Nodes = 15
Number of Edges = 100
>
>
> nodes(g1)
[1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O"
> degree(g1)
Error in degree(g1) : Not a graph object
>...gt; sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-unknown-l…
<div class="preformatted">Dear all,
I updated ChIPpeakAnno to 2.5.9 by:
useDevel(TRUE)
source("http://www.bioconductor.org/biocLite.R")
biocLite("ChIPpeakAnno")
After that, I got the following wrong Error information when starting
ChIPpeakAnno:
Loading required package: DBI
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
call: ls(envir, all.names = TRUE)
error: 7 arg…
updated 13.6 years ago • sheng zhao
Hi everyone,
I am trying to install Metab package (of Bioconductor) in R.3.5.1, but I am getting this error:
Attaching package: ‘xcms’
The following object is masked from ‘package:stats’:
sigma
Loading required package: svDialogs
Warning message:
__In fun(libname, pkgname) :__
__ mzR has been built against a different Rcpp version (0.12.19)__
_…
div class="preformatted">Dear all,
I am interested in identifying different chromosomal states
(gain,loss..) in
array CGH data.
Therefore I want to use the aCGH package, but I run into...some
problems.
(I have tested Version 1.04 (stable) and the developmental Version
1.0.6)
Maybe I can get some hints on how to proceed....
a) when I try to impute missing...gt;Error in solve.default(z$hessian…
div class="preformatted">Hello,
I think there may be a problem with the current version of
arrayQualityMetrics. I have downloaded two CEL files from GEO, read
them into
an AffyBatch object using the function...AB.Endoh
AffyBatch object
size of arrays=1002x1002 features (17 kb)
cdf=Mouse430_2 (45101 affyids)
number of samples=2
number of genes=45101
annotation=mouse4302
When I now call arrayQ…
updated 16.1 years ago • Joern Toedling
Hi all,
I had ChIPpeakanno installed and working on the last versions of R and Rstudio. I recently updated to the latest version or R and Rstudio. Just now I tried to run ChIPpeakAnno...Matrix, spatial
Warning message:
package ‘libmariadb-client-lgpl-dev’ is not available (for R version 3.4.3) </pre>
So now Im thinking I have to uninstall R vers…
updated 7.9 years ago • YaGalbi
and a data.frame containing for each
mutation whether it is exonic, intronic or intergenic, a gene
identifier
(possibly NA) and a GO identifier (possibly NA). ggbio accepts
GRange-class objects so I would like to merge the VCF...doing
this using the available R genomics packages?
Best wishes,
Stefan
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transfected with Gene 2
• samples co-transfected with, both, Gene 1 and Gene 2
There are two versions of the above 4 conditions at different temperatures, one set at 32C and one at 37C. When the 2 genes are expressed in...in parallel at 37C. It is the gene expression signature of the downstream signalling that we want to identify.
The original analysis plan to identify the gene expression…
updated 5.3 years ago • d.huntley
<div class="preformatted"> Hello,
I am exploring the idea of creating a package to import pathways as
BioPAX/SBPAX (Level 3) data to analyze various measurements. In
particular, differential microarray measurements could be used to
identify upstream pathway nodes that seem to play a critical role in
explaining the observed differences.
The basic idea is very simple: consider a pat…
updated 13.6 years ago • Oliver Ruebenacker
<div class="preformatted">Hello all,
I know the general question of "should I summarize/average/etc probes
that map to the same gene?" has been discussed many times before. But,
I
feel that it might be slightly different on the Illumina platform (at
least for the Mouse chip, which is the one I have been using).
For non-control probes, there simply is no advantage to using probe
summarized…
users/6aY5NGIpti0)) that there was a compatibility problem between the biomaRt package and BioMart versions 0.8 and 0.9, but it seems they were working on it.
Anyone knows if the issue has been solved?
Best,
Alex
<pre>
> sessionInfo...R version 3.4.3 (2017-11-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: defau…
I am trying to install dartR to work through at least part of “Introduction to dartR” tutorial.
I am running R version 3.5.1
My packages are up to date.
<pre>
> library(dartR)
Loading required package: adegenet...to install dartR to work through at least part of “Introduction to dartR” tutorial.
I am run…
I have been using the DESeq2 package for differential expression and have really liked the flexibility that the package provides for complex models including interaction effects. In one of the recent updates some of the interaction term functionality that I had been using has been disabled. Specifically, the ability to test one interaction term versus all others within the expanded model matrix f…
updated 10.1 years ago • marcus.stoiber
by 'quantmod':
method from
as.zoo.data.frame zoo
outlier cluster number: 2
convex hull cluster number: 2
Marker Gene Selection
A and S Matrix Estimation
Warning message:
In FUN(...) : Return NULL for...5: NULL
Any advice or feedback is greatly appreciated. TIA
> sessionInfo()
R version 3.6.1 (20…
updated 6.2 years ago • Matthew Thornton
for lazy loading
Warning in fun(libname, pkgname) :
mzR has been built against a different Rcpp version (0.12.3)
than is installed on your system (0.12.4). This might lead to errors
when loading mzR. If you encounter such issues
updated 9.7 years ago • ps1985
Hi,
trying to install package ‘BSgenome.Hsapiens.UCSC.hg38’ on R version 3.1.2.:
either
biocLite('BSgenome.Hsapiens.UCSC.hg38')
or
biocLite('BSgenome.Hsapiens.UCSC.hg38', dep=T, INSTALL...warnings()
Warning messages:
1: package ‘BSgenome.Hsapiens.UCSC.hg38’ is not available (for R version 3.1.2)
2: In install.packages(update\[instlib == l, "Package"\], l, .…
updated 10.3 years ago • kylvalda
Hello,
I am analyzing my results using DESeq2.
I have 3 conditions (0, 1 and 2 mL).
And I used this code to do the analys:
<pre>
> library("DESeq2")
> setwd("~/Documents/Trihar1")
> directory<-'/home/harumi/Documents/Trihar1'
> sampleFiles<-c("file1.counts","file2.counts","file3.counts","file4.counts","file6.counts", "file7.counts", "file8.c…
updated 8.2 years ago • Letícia
populations.
The successful applicant will need to have worked as a postdoctoral scientist for a number of years (at least 2 to 3) and have considerable experience of all standard molecular genetics and genomics techniques...data. We are looking for someone who can mine next-generation sequencing data creatively, to identify mutations associated with a variety of inherited diseases and…
updated 9.8 years ago • recruitment
<div class="preformatted">I'm trying to understand and analyse a microarray experiment performed
by someone else, and I've been reading about experimental design in
some books and have a few questions.
The experiment involves groups of animals assigned to one of 3 time
points (measured as the number of days since treatment) and
administered with either A or B treatment. 2 out 3 tissue samp…
updated 17.2 years ago • Nathan.Watson-Haigh@csiro.au
<div class="preformatted">
Hi guys,
I'm new on R and Bioconductor packages so my question can sounds a
little basics but I really could not figure out how to use a database
from NCBI in BiomaRt.
I'm working on RNA-Seq reads to perform DE analysis and I'm interested
in Bos taurus database from NCBI version UMD3.1.
So my question is: how to choose the bovine UMD3.1 from NCBI in
BiomaRt? Or t…
updated 11.8 years ago • Guest User
<div class="preformatted">Dear list,
Im trying to find differential expression between two conditions, as
well as within a condition over time. The data are RTqPCR, log10
relative expression of 96 genes (by 55), under 2 conditions, at 8
unevenly spaced timepoints with some missing data (NA) and variable
number of replicates (2-3):
nReplicates <- c(3,3,3,3,3,3,2,3, 2,3,2,3,2,2,3,3)…
updated 11.4 years ago • Linus Schumacher
Hello,
I hope this is the right place to report the issue. I was testing out GEOmetadb and found that gds in the 2023-06-26 version was empty (see below). In short, I downloaded the full GEOmetadb.sqlite and queried table gds, but found 0 records. I also tried to query gds from GEOmetadb_demo.sqlite and got 3566 records, which seems to worked perfectly well. So it looks like that the 2023-06-26 …
updated 2.5 years ago • malat1_t
biological
replicate samples. Unfortunately, our final eighth timepoint had to
be
hybridized to version 2.0 arrays, while all our other samples were
hybridized to version 1.0 arrays. We have found no way to normalize
these...on
the 3
replicates from the final timepoint, but find when I do this that I
end up
with vast numbers of identical values in the dataset. These are
highly
correlated (98-9…
updated 15.7 years ago • Kaitlin Louise Bergfield
div class="preformatted">Hello list,
While checking my scripts against the new R/BioC versions, I
encountered the following unexpected behaviour. Please consider the
following peace of code:
library(simpleaffy...gt; x
AffyBatch object
size of arrays=1002x1002 features (14 kb)
cdf=Mouse430_2 (45101 affyids)
number of samples=6
number of genes=1004004
annotation=mouse4302
notes=
> feat…
updated 18.6 years ago • Groot, Philip de
div class="preformatted">If you are planning on using that number of chips, at the moment the
only recourse is to use a 64 bit architecture which will allow you to
use more than 4 Gb RAM...using justRMA I bet you will not be able
to
do more than 50 - 60 of the version 2 chips with only 1 Gb RAM.
Best,
Jim
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan...probes…
updated 21.5 years ago • James W. MacDonald
I am trying to analyze the differential peaks in my ATAC-seq data. I have ATAC-seq analysis on 2 biological conditions with 3 replicates in each condition. Below is my sample info:
```
ID Factor Condition Replicate Intervals
1 ATACctrl1 ctrl1 ctrl 1 8654
2 ATACctrl2 ctrl2 ctrl 2 6750
3 ATACctrl3 ctrl3 ctrl 3 5962
4 ATACe…
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 this by mapping through
the EntrezIDs:
# mapping through eg ids...that ends in a numeric
part (eg Ensembl ids).
It is useful to return a mapping showing the original identifier, the
EntrezID mapped through and the required identifier so h…
with the agilent data
-Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature
Number
version).The gProcessed signal has been deposited as a series matrix
file in
Geo. I wanted to know if one can directly...can perform cyclic loess normalization?
Thank you in advance,
Viritha
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updated 15.1 years ago • viritha kaza
data
AffyBatch object
size of arrays=1164x1164 features (10 kb)
cdf=HG-U133_Plus_2 (54675 affyids)
number of samples=12
number of genes=54675
annotation=hgu133plus2
notes=
> eset<-rma(data)
Background correcting
Normalizing...data) :
VECTOR_ELT() can only be applied to a 'list', not a 'character'
*
*> sessionInfo()
R version 2.9.0 (2009-04-17)
i686-pc-linux-gnu
locale:
LC_…
updated 16.4 years ago • anupam sinha
to be much more seamless. ?For example, we don't
> particular like that we are requiring an old version of Graphviz,
but
> we have had problems with newer versions of GRaphviz on _some_
> versions of Windows (for example
this is abnormally large:
`` head(ddsTxi) ``
class: DESeqDataSet
dim: 6 635
metadata(1): version
assays(2): counts avgTxLength
`` dds <- DESeq(ddsTxi) ``
estimating size factors
Note: levels of factors in the design...contain characters other than
letters, numbers, '\_' and '.'. It is recommended (but not required) to use
only l…
Frameworks/R.framework/Resources/include" -DNDEBUG -DWITH_THREADS -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local...ERROR: compilation failed for package ‘WGCNA’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/WGCNA’
Warning in install.package…
updated 5.6 years ago • 562125035
<div class="preformatted">Hi all
I am new to R and have been using it for Illumina Infinium Methylation
450 k
Array analysis using the lumi package.
After normalization, I tried to identify differentially expressed
genes
using the example illusrated in the lumi PDF but look like during
lmFit, I
keep getting the same error and hence, I cant move forward.
*Error Message : *
> fit &a…
updated 14.6 years ago • Jasreet
Hi, I found there is no `` import.bam `` function in the latest version (1.22.3) of CAGEr. However, the import.bam function has been documented in the reference manual of CAGEr (<http://www.bioconductor.org...manuals/CAGEr/man/CAGEr.pdf>)
<pre>
> library(CAGEr)
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bi…
updated 7.2 years ago • Pengcheng Yang
identical to 'seqlevels(x)'__
I recently updated my OS and installed R and Bioconductor more recent versions. Today I have TEQC 4.2, R 3.5 and Bioconductor 3.7.
It used to work perfectly with TEQC 3.16, R 3.4 and Bioconductor 3.6
with around 24 conditions belonging to 6 different
groups with its first column containing the tag identifiers and the
other columns containing the read counts. I used read.delim function
in R in the following manner :-
seq_data...works. Please suggest where I am going wrong
thanks & regards
Saad
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an Annotation package for "pd.110916.mtub.h37rv.im.exp.til" built with
pdInfoBuilder, and I 've identified some DEG's.
Now I would like to do Gene Ontology and GSEA with these genes.I know
I
have to use these library(GOstats...CNRS
BP 64182
F-31077 Toulouse Cedex France
Tel +33 (0)5 61 17 54 63
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</div
updated 13.2 years ago • Ingrid Mercier
div class="preformatted">Hi all,
this a pretty general question ...
let say I have identified a set of genes differentially expressed
between
group A and group B and I m using Affy chips (but this could be also...enought... ?
Hoping that all this is understandable...
Thanks
Philippe
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