do
this if we have replicates and are using statistical tests - rather
than just fold-changes - to identify 'interesting' genes. Does the
statistical testing do this job for us?
Hi,
In my opinion you should always do some sort...non-specific filtering as filtering without reference to
phenotype (of any sort).
There are a number of reasons for doing this, some motivated by the
biology an…
Order by: Relevance
below). The last time these were updated was for Bioconductor 2.8 (3 years ago). We've tried a number of times to contact Francesco but did not get a response.
The plan is to remove these 24 from the Bioconductor 3.5 release...Keywords: utilities datasets
>
> ### ** Examples
>
> ## Count the number of rows in the "probes" table:
> dbGetQ…
start", "end"), :
The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing...0" cellspacing="0" style="width:1010.37px">
<tbody>
<tr>
<td>
<pre>
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-…
updated 9.2 years ago • iyerl
R link makes it sound like it's on a DESeqDataSet (https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/collapseReplicates).
Previous posts on this haven't really clarified this.
I've unsuccessfully transformed...DESeqDataSetFromMatrix derived dds matrix (code below), so I'm sure it's that; I get the expected number of columns reduced based on the number of replicates I have…
updated 6.3 years ago • wiscoyogi
<div class="preformatted">Post the header of the unsuccesful gpr file
-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of alison
waller
Sent: Fri 30/11/2007 9:13 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Limma - error reading in .gpr files
Hi all,
I'm having a problem reading in my genepix files using read.maimages.
If
anyone could help int…
from vignette source 'cosmo.Rnw'
###################################################
### code chunk number 1: load
###################################################
library(cosmo)
.... according to the R script ...
###################################################
### code chunk number 17: example1
###################################################
seqFile <- system.file("Exfiles/s…
TORAFFAE/R_projects/Pine
Microarray/pd.110224.pinus.fa.exp.modified.zip' is not available (for
R version 3.0.2)
Installing package into 'C:/Rlibs/3.0.2'
(as 'lib' is unspecified)
>sessionInfo()
R version 3.0.2 (2013-09-25)
Platform...Helsinki
Department of Forest Sciences
Latokartanonkaari 7 PO Box 27
00014 Helsinki (Finland)
Phone number: +358 9 191 58136
email: tommaso.raffaello@helsin…
updated 11.7 years ago • Tommaso Raffaello
I am finding overlapping region in two chipseq samples. The number of overlapping peaks in ven diagram are different from what you get in ol1$overlappingPeaks and ol1$peaksInMergedPeaks...For specific peak the ven diagram number is same as in ol1$peaklist. But not for overlapping peaks.
In example data provided by tool, I found same number in
updated 8.7 years ago • sudhirjadhao2009
Bioconductor 2.7:
1. Install R 2.12.0. Bioconductor 2.7 has been designed expressly for
this version of R.
2. Follow the instructions here:
http://bioconductor.org/install/
Please visit http://bioconductor.org for details...Models
IsoGeneGUI
A graphical user interface to dose-response analysis of microarray
data
les
Identifying Loci of Enhanced Significance in Tiling Microarray D…
updated 15.2 years ago • Martin Morgan
1. There are two ways to use less memory in dba.count. The best way is
to update to the latest version of DiffBind in Bioconductor 2.12.
dba.count now has a parameter to do the counting with less memory (but
a bit slower...You can set bParallel=FALSE to do this -- it is
a lot slower though! You can also try to lower the number of cores
being used when it runs in parallel, e.g.
> DBA$confi…
packages that are only available in Bioc3.1, so annoyingly there's no simple way to just use the old version)
The single sample sample sheet looks like this:
<pre>
Sample Input SampleID Factor Replicate Num_peaks
1 CTCF_Cuddapah_sorted.bam...2: fragmentlength(res)
1: ChIPQC(sample_sheet[1, ], chromosomes = "chr1")
sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-…
updated 10.4 years ago • liz.ingsimmons
in data.frame(x1 = start(pairGaps) - 1, y1 = gy, x2 = end(pairGaps) + :arguments imply differing number of rows: 0, 1
# Note that if I set isPaired to FALSE instead, then the plot works (but this is not what we want to do)
fusionReadsAlignment2
updated 8.0 years ago • stianlagstad
described: hist(), image(), boxplot() and RNA
degradation plots.
Has anybody used these methods to identify bad quality chips? When do
you exclude a chip from further analysis? What's your decision rule?
Any other suggestions...on how to identify bad quality from the data
alone?
Thanks a lot.
-oli-
--
Oliver Hartmann, Institute of Medical Biometry and Epidemiology
updated 22.8 years ago • Oliver Hartmann
new.dil
AffyBatch object
size of arrays=640x640 features (6405 kb)
cdf=new.dil.cdfenv (12453 affyids)
number of samples=2
number of genes=12453
annotation=hgu95av2
> length(pm(new.dil[,1]))
[1] 12453
As noted above, I have 12453 probe...Hence, the probe that I'm interested in may not be matched to the
correct one.
The versions I'm using:
R: 1.9.0
altcdfenvs: 1.0.0
affy: 1.4.31
ath112150…
updated 21.1 years ago • Hee Siew Wan
output
below),
since data were collected with a custom Agilent microarray. Using the
most
updated version of the arrayQualityMetrics package (downloaded
yesterday,
16 October 2013), it gives the error "undefined columns...arrayQualityMetrics(expressionset=sponge_ExpressionSet,outdir="report
1",force=TRUE,intgroup=c("Chip Number","Hyb Date"))The report will be
written into directory 'report1'. Err…
updated 12.1 years ago • Lisa Cohen
mdc-berlin.de>
Date: Tue Oct 24 20:22:47 2017 +0200
update news and bump version number
commit ae86509371d40dc536766b72e1919839986393d4
Author: Alexander Gosdschan <alexander.gosdschan...mdc-berlin.de>
Date: Tue Oct 24 20:22:47 2017 +0200
update news and bump version number
commit ae86509371d40dc536766b72e…
of Locus IDs, e.g., NM_001533, BC001721, ., are
there
any Bioconductor packages that "connect" these identifiers to gene
ontology
identifiers, or perhaps some other identifier (say LocusLink, aka
Enterez
Gene) that is mapped
<div class="preformatted">New Year greetings to all.
I have a problem which I am not sure how best to solve, and hope to
seek advice from the list.
I have 200 oligonucleotide arrays of about 13000 transcripts,
belonging to approximately 6 different cancer subtypes. Essentially, I
am hoping to first identify "gene modules" of gene expression
corresponding to a specific cancer subtype, or g…
updated 20.9 years ago • Min-Han Tan
coef=1, p=0.05, lfc=2, n=1000, adjust="BH")
I will get an error
Error in M[sig, ] : incorrect number of dimensions
However, if I change the command to
TB <- topTable(fit3, coef=1, p=1, lfc=0, n=1000, adjust="BH")
It works fine.
So, it...like the error comes up whenever I need to cutoff some of
the probes.
Here is my sessionInfo:
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
locale:
L…
updated 17.1 years ago • Chen, Zhuoxun
to a Mutiple Series Time Course Microarray design, for which
also Real Time -PCR data for a number of genes has been measured.
Can anyone put me in contact with such a data set?
Thank you in advance.
Mar?a Nueda
PhD Student...Statistics and Quality
University of Alicante
Spain
email:mj.nueda at ua.es
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.6 (GNU/Linux)
Comment: …
updated 18.6 years ago • Ana Conesa
raw data
(cDNA) already has intensity levels linked to a gene and not some
arbitarary code number.
Could any one please post their understanding about annotated data.
thank you.
Ranga
---------------------------------
[[alternative HTML version deleted
updated 21.5 years ago • Ranga Chari
<div class="preformatted">
This will manifest itself by seeing the error message
Error in aqm.highlight(doc, annotationInfo = annotationInfo) :
'length(annotationInfo$annotation)' must be equal to
'length(series)', the number of objects in the plot.
The reason appears to be a misfit between R's SVG-device and the
package
SVGAnnotation that seems to have entered just a few days before
R…
updated 15.1 years ago • Wolfgang Huber
input field exceeds buffer length
However the data seems to load when I set a limit for the number of
SNPs:
x=read.impute("chr1.gen",nsnp=200)
Does anyone know what this error means? Is it expecting maybe a subset
of
the...have encountered this error before please let me
know.
Thank you
-fra
[[alternative HTML version deleted]]
</div
div class="preformatted">Hi -
There are a number of people in our branch and potentially at NIH
interested
in using bioconductor for microarray analysis. I was wondering...Bethesda, MD. 20889-5101
(301) 435-5436 - phone
(301) 496-0047 - fax
[[alternate HTML version deleted]]</div
updated 22.6 years ago • Joshi, Nina NIH/NCI
a test to check for multi-modalities in histograms?
* Is there a way to know the cells and the number of values per
cell
used by hist to check for multi-modalities in a rudimentary way?
Thanks again,
Javier
[[alternative...HTML version deleted]]
</div
updated 15.7 years ago • Javier Pérez Florido
<div class="preformatted">Hi List,
I have two questions:
1)
I have a chip which is the same feature as u133A, however have much
less mm
probes. When using pm or mm method, the matrices have the same
dimension. I
wonder, do the methods assume the number of probes for pm or mm are
the
sames by default? How do you determine pm or mm probes?
2)
The cdf I am using is the same size as...usi…
in an array using
limma package. each gene is printed twice on an array.
For example, the actual number of genes is 19000 in my dataset, since
there are replicate genes, I have 38400 spots (genes) in my dataset.
I am just wondering...Post your free ad now! Yahoo! Canada Personals
[[alternative HTML version deleted]]</div
loess method.
normalize.loess(data,epsilon=1,log.it=F,span=0.4,maxit=4).
As I understand that the number of iterations (maxit) should be
performed
until there is no convergence.
1) Would it make a difference if I log and do the...dataset by cyclic loess?
Waiting for your reply,
Thanks,
Viritha
[[alternative HTML version deleted]]
</div
updated 14.9 years ago • viritha kaza
would be willing to share the experience.
I have about 100 mouse SNPs in the format:
Chromosome number SNP coordinate
(for example:)
16 69067865
I need to annotate them, in order to understand whether they are
functional...else.
I would really appreciate your suggestions!
best regards
Galina
[[alternative HTML version deleted]]
</div
updated 15.3 years ago • Glazko, Galina
<div class="preformatted">---------- Forwarded message ----------
From: Áõΰ <antibodyliu@gmail.com>
Date: 2012/12/20
Subject: Re: [BioC] bout big data set for Affy R packge
To: "James W. MacDonald" <jmacdon@uw.edu>
Hi Jim,
Thank your reply. As far as I know, affy is not very suitable for
MoGene-1_st-v1 chip (I do not validate, but get the information from
internet). Actu…
<div class="preformatted">Dear edgeR community,
Good day.
I can learn summary of the up and down regulated genes/tags from
>summary(de <- decideTestsDGE(lrt))
when the *coef *of *glmLRT*(the likelihood ratio test) is set to one
degree
of freedom.
When the *coef* is set to i.e. 2:5; the decideTestsDGE doesn't work.
It
could be nice to see the summary of up and down regulat…
Dear BioC Users,
Version 1.4 of [`` epivizr ``](http://www.bioconductor.org/packages/release/bioc/html/epivizr.html) was released as part...Bioconductor 3.0 release](http://master.bioconductor.org/news/bioc_3_0_release/). There are a good number of new features in `` epivizr `` in this release, including the ability of running the visualization UI _wi…
updated 11.1 years ago • Hector Corrada Bravo
<div class="preformatted">Hello,
What limits the number of sequences and size of sequences that are
part of a DNAStringSet? Are there any way to change these limits?
On my home laptop I can create a DNAStringSet of about sixty thousand
sequences of length 1500. On my desktop I can only make a
DNAStringSet of twenty thousand sequences. Does anyone know what is
creating this difference i…
updated 15.5 years ago • Erik Wright
i) file-size of
the bam file and (ii) the available memory.
Can I somehow pinpoint (e.g. file-size, number of alignments, memory
requirements) when it is more efficient ( = faster and memory
requirements are feasible) to process...batch or,
alternatively, do it in an iterative manner?
Best,
Stefanie
[[alternative HTML version deleted]]
</div
I) for network construction. [A total of 18 modules were generated][2]. Next, I would like to identify top hub gene in each module.
If I followed the [previous post][3], more that 18 hub gene were identified which is not really...Hence, I would like to know if the correct way of identify hub gene should be as below?
````````````````
moduleLabels = net$colors
moduleColors = labels2colors(ne…
updated 3.7 years ago • wes
slight difference on number of differential expression gene in limma from topTable() vs Volcano plot
I find some funny stuff when I check out the DEG number by two ways in limma.
It's multiply time points study. TP1, TP2, TP3......
The first way is very conventional as:
\# Create a design...I find some funny stuff when I check out the DEG number by two ways in limma.
It's multiply time points study. TP1, TP2, TP3......
The first way is very conventional as:
\# Create a design matrix
tim…
updated 8.7 years ago • joseph
of data and I got a little trouble:
After apply fitmaanova, was showed the message:
Finish gene number 3500 ...
Error in next.fix:(next.fix + ncols - 1) :
NA/NaN argument
Here is my experiment layout:
Strain = 2 (sensible; tolerant)
Treatment...Calculating variance components for fixed model...
Fitting mixed effect model...
Finish gene number 100 ...
(...)
Finish gene number 3500 ...
…
<div class="preformatted">The genetics lab of Prof. Sir Bruce Ponder and the computational
biology lab of Dr. Florian Markowetz offer a joint position for a
postdoctoral researcher interested in statistical and computational
approaches to systems genetics in breast and lung cancer.
The position bridges between an experimental and a computational lab
and is ideal if you are interested in da…
into the 3' adaptor sequence that must be trimmed.
The solution we are currently working on is to identify the minimal
sequence that is recognizable as the adaptor sequence and trim that
using trimLRPatterns() in the Biostrings...Post-doctoral Fellow
Fred Hutchinson Cancer Research Center
206-667-5544
[[alternative HTML version deleted]]
</div
updated 12.4 years ago • Taylor, Sean D
Specific tasks include integrating and mining historical data, and
developing new methods for identifying mechanisms of actions related
to toxicity in preclinical setting.
Requirements: A Masters or Ph.D in Bioinformatics...such as microarrays and programming with Matlab or R is
also expected.
[[alternative HTML version deleted]]
</div
updated 15.4 years ago • Taylor, Scott
preformatted">Hi All,
I am working on sRNA-seq data and with no replicates and using edgeR
to
identify differentially expressed tags and using an arbitrary BCV
value
(0.3) based on suggestion in edgeR manual:
"Simply...arbitrarily?
I would really appreciate any help. Awaiting reply.
Atul
[[alternative HTML version deleted]]
</div
egs)
#gives [1] "character" - so I'm quite confused now.
NA %in% egs
#gives [1] TRUE
How do I identify which entries in 'egs' are NA so I can remove them?
It's trivial here but the dataset I'm working with is in the
thousands...Thanks
iain
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TI…
updated 14.4 years ago • Iain Gallagher
div class="preformatted">Hi Dick,
I believe the problem is fixed in the version of simpleaffy in the
Devl
branch (2.07). I'll also update the release version - in the meantime
try the version from the...exp1.all.raw
AffyBatch object
size of arrays=712x712 features (51493 kb) cdf=MOE430A (22690 affyids)
number of samples=13 number of genes=22690 annotation=moe430a
exp1.mas5 <- call.expr…
updated 20.9 years ago • Crispin Miller
BTW, I tried to update AnnBuilder package with
biocLite('AnnBuilder') all I got is still the old
version, AnnBuilder_1.10.0, I am not sure exactly how
to get the updated version AnnBuilder_1.10.1, as
suggested by Nianhua...baseMapType =
myBaseType,
pkgName = "hs95av2Entrezg7", pkgPath = myDir,
organism = "Homo sapiens", version = "1.1.0", author =
list(authors = "Weijun",
maintainer = "Weijun <…
updated 19.4 years ago • Luo Weijun
Hi,
I want to obtain read counts at the exon level using featureCounts. I run Rsubread and use these options:
annot.ext="/home/inah/RefGTF/GRCh38/annotation/Homo\_sapiens.GRCh38.85.gtf",
isGTFAnnotationFile=TRUE,
GTF.featureType="exon", GTF.attrType="exon\_id", useMetaFeatures=FALSE
The resulting count matrix has 1,182,163 rows but only 678,276 unique row i…
updated 8.5 years ago • inah
Hello,
I have a “xlsx” quantitative dataset from proteome discoverer software (the xlsx matrix file contains rows as identified proteins and columns as different conditions/treatments, and matrix cells corresponds to spectral counts).
I need to convert my xlsx dataset to MSnSet format to be able to use msmsTests package for identifying differentially expressed proteins (probably msmsTests a…
updated 6.8 years ago • fgol
at multiple time points, and we have done :
-- the standard scRNA-seq analysis in order to identify the cluster specific markers and
-- the standard scRNA-seq analysis in order to identify the differential markers
updated 5.4 years ago • Bogdan
<div class="preformatted">Yanara,
As Jianhong mentioned already, increasing totalTest will lead to a
smaller p-value. Here is a previous post that might be helpful to you.
Thanks!
https://stat.ethz.ch/pipermail/bioconductor/2010-November/036540.html
Best regards,
Julie
On 7/5/13 9:04 AM, "Ou, Jianhong" <jianhong.ou@umassmed.edu> wrote:
Hi Yanara,
Do you mean you have already fi…
updated 12.4 years ago • Julie Zhu
paste0(root, url, "/", files[grep("MANIFEST", files)]), :
Unable to find 5 lines with expected number of columns (+ middle)
2: In fread(paste0(root, url, "/", files[grep("MANIFEST", files)]), :
Unable to find 5 lines with expected number of...paste0(root, url, "/", files[grep("MANIFEST", files)]), :
Unable to find 5 lines with expected number of columns (+ middle)
2: In fread(paste0…
updated 9.4 years ago • mukhamadeeva.r
many thanks
Problematic code:
```r
> d
class: DEXSeqDataSet
dim: 414939 914
metadata(1): version
assays(1): counts
rownames(414939): X_153693905_153694633:X_153693905_153694633 X_153693905_153694633:X_153693905_153694633.1...MulticoreParam(workers = 54, progressbar = TRUE))
```
R session info:
```r
> sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu…
updated 4.7 years ago • Angel
NA_character_,
NA_character_
)
)
, metadata = list()
)
>
[[alternative HTML version deleted]]
</rle></iranges></rle></div
updated 13.0 years ago • Hermann Norpois
Dear Bioconductor community,
except the analysis i have performed to identify potential master regulators in one microarray dataset i have analyzed, i would also like to perform __some kind...of TF-binding site analysis /& promoter analysis__ to also identify __enriched TF-binding sites__(which could also strengthen my results for the possible TFs i have identify) and also
updated 10.5 years ago • svlachavas
<div class="preformatted">Hi Shilin,
The confusion is in the groups. Data columns 1-4 are paired with
columns
5-8 respectively, as you have identified. However, there is a further
structure to the data, which is that the first two paired samples are
biologically distinct...confusion is in the groups. Data columns 1-4 are paired with
columns
5-8 respectively, as you have identified. However…
<div class="preformatted">On Mon, Oct 11, 2004 at 02:18:26PM -0400, Saurin D. Jani wrote:
> Hi BioC,
>
> I am using R-2.0 on Fedora Core 2 LINUX. I went to Bioconductor and
I could not
> find latest GO verstion, it has only GO_1.5.1.tar.gz.
>
> > getRversion()
> [1] '2.0.0'
>
> > library(annaffy,warn.conflicts = …
updated 21.2 years ago • rgentleman
cancercenter.columbia.edu
> http://cancercenter.columbia.edu/~friedman/
>
> "Complex numbers! Ha! Ha! There is nothing weirder
> than imaginary numbers. Architects don't need to know
> complex numbers. Whenever...gt;
>
> I appreciate any help.
>
> Best Regards,
> Chris
>
> [[alternative HTML version deleted]]
&…
Dear All,
I have some problems running my script with the latest version of ChIPQC1.12. The script was working well on the older version of the package. I was wondering if someone else is also
nbsp; calculating background for <X\_8\_\_HuGene\_2\_0\_st\_.cel>...
Error: Number of PMs or MMs is zero.
An error has occured: Need to abort current process.
Error in .local(object, ...) : error in rwrapper function
updated 9.8 years ago • Biologist
<div class="preformatted">Hi everybody.
As a newbie to bioinformatics, it is not uncommon to find difficulties
in the way biological knowledge mixes with statistics. I come from the
Machine Learning field, and usually have problems with the naming
conventions (well, among several other things, I must admit). Besides,
I am not an expert in statistics, having used the barely necessary for
th…
what I will end up with is essentially a one-class
>experiment. In other words, I would like to identify groups whose
>summary D-statistic (I recognize from the recent literature that
there
>is more than one summary...gt;whose average D-statistic is different from zero. I am advocating
using
>a t-test with n=number of experiments with corresponding degrees of
>f…
I want to run DESeq2 to identify differences in open chromatin accessibility (i.e. ATAC-seq data) between 3 different GROUPS: A, B and C. I also wanted...what method is more appropriate. Note that I used the same ATAC-seq counts files (i.e. the total number of sites was the same) for both analysis methods.
Method 1: Combining all groups, using LRT while running DESeq2 to control
updated 6.8 years ago • jonathan.diedrich
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
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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
by
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43k
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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43k
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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The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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