e.g. norm-
exp
in limma. We did not have this type of distribution in version 3 of
HT12,
nor in any other chip type from Illumina. Has anyone else seen this
particular issue, and specifically on the HT-12 v4 chip?
Below
Order by: Relevance
design = m1)```
but when I tired to make the results, I couldn't find ```disease_muta_vs_Control``` nor ```disease_mutb_vs_Control``` in ```resultNames()```.
This is the results of the resultsNames()
```
resultsNames(dds)
[1] "Intercept" "diseasemuta
NULL,
subtitle = NULL,
caption = NULL,
xlab = bquote(~Log[2]~"(Fold Change)"),
ylab = bquote(~-Log[10] ~ "(" * italic(P[adj]) * ")"),
drawConnectors = TRUE,
pointSize = 1.2,
colAlpha = 0.5,
colCustom = keyvals,
arrowheads
updated 2.8 years ago • Peter
sampleNames(SpikeIn)), 20, 12,
byrow = TRUE)
par(mfrow = c(1, 2))
matplot(concentrations, pms, log = "xy", main = "PM", ylim =
c(30,20000))
lines(concentrations[1, ], apply(pms, 2, mean), lwd = 3)
matplot(concentrations, mms, log = "xy", main = "MM", ylim =
c(30
y)\[as.logical(de)\]
plotSmear(et, de.tags=detags)
pdf("Volcano\_Plot.pdf")
plot(raw$logFC,-log(raw$PValue,10),
xlim = c(-6,6),ylim = c(0,9),
col=ifelse(abs(raw$logFC)<=2 | -log(raw$PValue,10)<1 ,"black
updated 10.1 years ago • Sushant Pawar
<div class="preformatted">hiii
please check out this following error...and let me know where am going
wrong....
> outdir = "C:/Users/neurooncolab new pc/Documents/R"
> me <- "Wolfgang Huber <w.huber@dkfz.de>"
> species <- "Homo_sapiens"
> species <- "Homo_sapiens"
> makeProbePackage("HG-U95Av2", datafile = gzfile(filename, open…
updated 16.0 years ago • sneha patil
sampleNames(SpikeIn)), 20, 12,
byrow = TRUE)
par(mfrow = c(1, 2))
matplot(concentrations, pms, log = "xy", main = "PM", ylim =
c(30,20000))
lines(concentrations[1, ], apply(pms, 2, mean), lwd = 3)
matplot(concentrations, mms, log = "xy", main = "MM", ylim =
c(30
x <- as.matrix(x)
if (is.null(lib.size))
lib.size <- colSums(x)
if (log) {
prior.count.scaled <- lib.size/mean(lib.size) * prior.count
lib.size <- lib.size + 2 * prior.count.scaled
}
lib.size <...1e-06 * lib.size
if (log)
log2(t((t(x) + prior.count.scaled)/lib.size))
else t(t(x)/lib.size)
}
Kind regards,
V…
updated 11.4 years ago • Vang Le
1]: https://www.bioconductor.org/help/education-training/
[2]: https://bioconductor.github.io/2022-09-12-BiocIntro-Heidelberg/
[3]: https://us06web.zoom.us/j/87341275965?pwd=Tm1LUEVPUHRxQUdLZHBJL3VQV1lZUT09
[4]: https
updated 3.4 years ago • Laurent Gatto
how to work this out...
Output of >sessioninfo()
```
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.0.1
Matrix products: default
BLAS: /Library
updated 3.3 years ago • sebast1an
command console formats
Any help would be much appreciated !
sessionInfo( )
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale
celeganscdf_1.4.3.tar.gz has been built (if working) and
checked for Windows.
Please check the log files and (if working) the binary package at:
http://win-builder.r-project.org/d55nO2ykFkHm
The files will be removed after
updated 16.8 years ago • Uwe.Ligges@r-project.org
I am trying to analyze microbiome data, which is count data with many zero-counts. <span style="line-height:1.6">I receive this error when I run the DESeq function in DESeq2:</span>
<pre>
estimating size factors
Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc, :
every gene contains at least one zero, cannot compute log geometric mean…
updated 9.5 years ago • pjgalli2
Hi,
I wish to draw a RLE plot from my expression dataset which already is
preprocessed and has log transformed values. Is there an inbuilt
function ( apart from the one in affy package that uses a PLMset )
that can calculate
preformatted">Can I suggest that limma package returns the posterior probabilities
along with the log odds ratio, B ?
I am currently using the following codes to get the posterior values
(unless I am reading the documents wrong
I figure out a 10% difference in methylation in M-value space for a cutoff? - (This may just be log space doing a number of my brain on a friday afternoon!)
Has anyone got any advice
I'm using the timecourse package in bioconductor. I have been obtaining size factors for each of the samples from DESeq's sizeFactors() before log transforming the raw data and using this in mb.long() from timecourse.
<span style="line-height:1.6">Should I be doing this or...I have been obtaining size factors for each of the samples from DESeq's sizeFactors() before log transforming the ra…
updated 11.2 years ago • b.curran
the data are calibrated, do limma (if this is the best
method) and
simple t-test (test of the log transformed intensities) give very
different
results?
Thank you,
Makis
----------------------
E Motakis, Mathematics
E.Motakis at bristol.ac.uk
working on a project with a binary outcome, and need to report beta coefficients (representing the log-odds increase per copy of the minor allele), confidence intervals, and odds ratios for each variant. I am using a SeqVarGDSClass
updated 6.8 years ago • Stephanie M. Gogarten
has been
built (if working) and checked for Windows.
Please check the log files and (if working) the binary package at:
http://win-builder.r-project.org/G0F49W9lU0ez
The files will be removed after
updated 13.2 years ago • Uwe.Ligges@r-project.org
Hi I'm using Star align and the build in htseq to count gene features.
however I notice that the final log file, specifically "Uniquely mapped" does not matched the total library size of the count. For example, I could have sample...Star align and the build in htseq to count gene features.
however I notice that the final log file, specifically "Uniquely mapped" doe…
updated 8.4 years ago • Ahdee
them because, as I read from the gcrma paper,
the
expression values after the gcrma() routine are log(intensity) after
background
adjustment.
My question is: Do I have to convert the expression values from
gcrma() back to
raw
half of my samples have been flagged and not included in the plot. I have not uploaded any screen log file. Additionally, 'screen description' tab contains no description loaded. The plate layout visualization seems fine
updated 10.5 years ago • mdutra
have aligent CGH data i have download the raw file as well as series matrix file in which they have log value but they do not have probe name.. how to read and normalized the data that is not clear with me...i have seen in limma package
updated 9.8 years ago • sainiisha22
for processing the bead level data? I like the idea of
summarizing in log2-space but I want a non-log-space result to use
with
vst. Is there a simple way to accomplish this?
And while I'm asking this, I seem to remember hearing
updated 16.7 years ago • Cei Abreu-Goodger
**Bioinformatician Position: Brain Microcircuits in Psychiatric Diseases**
https://apply.bio.mx/job/2019-J04
**About BioMed X**
The BioMed X Innovation Center is an exciting new collaboration model at the interface between academia and industry (Nat Biotechnol. 2015 33(1):20-1). At our center, distinguished early-career scientists recruited from all over the world work jointly on novel pre…
updated 6.8 years ago • slezak
users would lack access to key elements of
> > the interface.
> > d) Commitment to public and open APIs sharply reduces
> > effort required to support multiple platforms. When compiled
> > libraries...As researchers
> > we cannot accept this additional cost.
> > e) Commitment to public and open APIs is the only…
<div class="preformatted">Hi,
We are trying to use beadarraySNP on Illumina sample files. We are
using R
2.9 with bioconductor 3.4.
Please, if any one can help us it would be most appreciated.
At this time we have access only to final report files, so we are
constructing
samplesheet manually based on the documentation:
[Header],,,,,,
Investigator Name,Test,,,,,
Project Name,Test,,,,,
E…
updated 16.5 years ago • Boris Umylny
PMC3378882/
In the edgeR code (glmfit.R):
logFC <- drop((glmfit$coefficients %\*% contrast)/log(2))
Where I guess the glmfit$coefficients are the beta(g) above and the "contrast" variable is the x(i) vector.
__Is this the same...formula? If not, what is the difference? If so, why is log(mu(gi)) = logFC?__
From http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378882/ again:
"We d…
updated 10.8 years ago • cpcantalapiedra
## Scientist, Computational Biology
[Denali Therapeutics](https://www.denalitherapeutics.com/home) is dedicated to developing breakthrough therapies for neurodegenerative diseases through our deep commitment to degeneration biology and principles of translational medicine.
We are looking for a Computational Biologist to join our Discovery Genomics team to study the biology underlying neuro…
updated 4.0 years ago • Thomas
the output of high-throughput runs for quality and
biological meaning
· Contributing to the publication of results
· Developing and publishing new analytical methods, where
needed
· Contributing to the CCDs software...Curriculum vitae listing education, qualifications, and
experiences, including a list of scientific publications
The information in this e-mail is inten…
updated 12.0 years ago • Wittner, Ben
<div class="preformatted">I am new to QuasR, and alos quite new to aligning short reads to
reference genomes more generally.
I cannot figure out how to use a pre-built indexed reference genome
file with QuasR. The examples supplied with the package work nicely.
Scaling up to using all of hg19 raises problems for me. I apologize
if I am missing the obvious.
To illustrate the problem, I c…
the output of high-throughput runs for quality and
biological meaning
? Contributing to the publication of results
? Developing and publishing new analytical methods, where needed
? Contributing to the CCD?s software...Curriculum vitae listing education, qualifications, and
experiences, including a list of scientific publications
The information in this e-mail is intended only …
updated 12.6 years ago • Wittner, Ben
the output of high-throughput runs for quality and
biological
meaning
* Contributing to the publication of results
* Developing and publishing new analytical methods, where needed
* Contributing to the CCD's software...Curriculum vitae listing education, qualifications, and
experiences,
including a list of scientific publications
The information in this e-mail is intended only …
updated 13.9 years ago • Wittner, Ben
<div class="preformatted">Several postdoctoral positions are available in Statistics, Machine
Learning, and Integrative Genomics within the Department of
Statistics, and the FAS Center for Systems Biology at Harvard
University, under the supervision of Professor Edo Airoldi.
We are seeking outstanding postdoctoral candidates from statistics,
machine learning, and computational biology, to …
Optimize usage of such tools and set up standard analysis
procedures
* Data acquisition from public databases and other online
resources
Skills:
* Knowledge of statistical methods
* Experience of statistical software...such as SPSS, S+ or R
* Strong experience in microarray data analysis
* Knowledge of public databases and other online biological
resources
Experience:
Maste…
updated 22.3 years ago • Sophie Gallina
<div class="preformatted">-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hi all,
This is not a proper Bioconductor question, but I think this is a good
forum to place my request. I am looking for a public/available dataset
regarding to a Mutiple Series Time Course Microarray design, for which
also Real Time -PCR data for...Bioconductor question, but I think this is a good
forum to place my…
updated 18.7 years ago • Ana Conesa
genes, clustering into subpopulations and marker gene detection. We demonstrate the analyses on public data sets involving haematopoietic stem cells, brain-derived cells, T-helper cells and mouse embryonic stem cells
updated 9.4 years ago • Aaron Lun
best wishes
Robert
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington
I have biology background and am just starting to learn Rstudio. I have made the database from the cuffdiff output from cufflinks. But now I need to visualize the data and get to meaningful figures for publications.
I have installed cummeRbund but I have zilch programming skills and am unable to understand the commands.
I...output from cufflinks. But now I need to visualize the data and get to …
updated 10.7 years ago • mfahim
We are looking for a highly motivated scientist to help drive a
development
of new pathway-oriented public bioinformatics software tools (see
www.GenMAPP.org). An ideal candidate will have a PhD or equivalent in
Computational
updated 22.6 years ago • Kristina Hanspers
is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version
designed to work primarily (only?) with well established model organisms that have lots of tracks publically available at e.g. UCSC. Before diving in any deeper I thought I'd ask, can I use our own assembly and models (which are
updated 6.2 years ago • martinson.john
data sets comparable to each other such that the analysis is biologically valid and accepted for publication. I could not find any online methods for this sort of analysis, though its been shown in many papers.
Thanks
2 123456_at 1234 2
4 12345678_at 12345 4
I hope one can help me out! I have seen this in several publications,
so
there must be a way.
Thanks in advance, Andreas Heider
[[alternative HTML version deleted]]
</div
A core part of the informatics team, the role will involve performing analyses of in house and public transcriptomic datasets and creating tools to improve data accessibility across the organization. Contributing
updated 4.9 years ago • m.jackson
Biology and Functional Genomics Laboratory
Center for Cancer Computational Biology
Harvard School of Public Health, Dana-Farber Cancer Institute (SM824)
Phone: +1 (617) 582 7267
Fax: +1 (617) 582 7760
Email: bhaibeka@jimmy.harvard.edu
CEL, CHP, CDF, BAR and BPMAP files. This souce code is
being provided
under the GNU Lesser General Public License (LGPL).
Click here to download the SDK
<a href="http://www.affymetrix.com/redirect/email.jsp?source=nl200412adn
on either
posting,
Robert
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington
Hello,
I am author of the oposSOM package and I wanted to update it to the latest version. Therefore I needed to link my newly created github accout following the HowTo "Create a new GitHub repository for an existing _Bioconductor_ package", step 3 "If you have an existing svn account, [submit your SSH public key](https://goo.gl/forms/eg36vcBkIUjfZfLe2) or github id to _Bioconductor"._
I used t…
updated 8.0 years ago • wirth
U133A chips (using R2.4dev downloaded yesterday on a PC with
winXPPro) which according to a recent publication in Bioinformatics is
more accurate than RMA / gcRMA etc...
Why is it that I get for more than 3/4 of the probesets the
therefore we get a better coverage
than getting
description from TAIR. When the "Representative Public ID" (or
"Transcript ID")
is a AGI locus id, it seems the description was retrieved from TAIR.
However, it
is not clear how this...home/tair/Ontologies/Plant_Ontology/stru-060
309.txt .
The pubmed ids represents the publications that TAIR used to map a AGI
locus id
to a concept in Plant Ontology.…
updated 19.4 years ago • Nianhua Li
by looking at spatial effects, but if you can see NO spatial
effects in either Rb, Gb, Rf, Gf or log(ratio) then I'm at a bit of a
loss.
Clearly you have a finger which represents spots that have higher Cy5
than Cy3. Clearly this...finger shows an unnatural relationship with
log(intensity). You are right to ask - is this a result of
unnaturally
high Cy5 or unnaturally low Cy3? Here's what I w…
updated 21.5 years ago • michael watson IAH-C
counts(object), locfunc = locfunc, :
every gene contains at least one zero, cannot compute log geometric means
I've managed to get the script running but only if I include the geomeans function:
MERGED_nonsinglet.age.dds...MERGED_nonsinglet.age, ~ Age_class)
gm_mean = function(x, na.rm=FALSE){ exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x))}
geoMeans = apply(counts(MERGED_…
updated 6.2 years ago • watsons2
mart = mart36)
[1] non-BioMart die(): Cannot write to '/ensemblweb/tmp/archives/54/logs/biomart-log4perl.log': No space left on device at /localsw/perl-5.8.8/lib/site_perl/5.8.8/Log/Log4perl/Appender/File.pm
updated 5.7 years ago • g.hemani
dds).
And I get error saying every gene contains at least one zero, cannot compute log geometric means.
Now i want to use pseudocount. Although I don`t know how to write the script. Could you please help
updated 3.5 years ago • nafsa
package Rsamtools_1.0.8.tar.gz has been built (if working) and
checked for Windows.
Please check the log files and (if working) the binary package at:
http://win-builder.r-project.org/ajc9sal7cw5x
The files will be removed after
updated 14.4 years ago • Uwe.Ligges@r-project.org
use toptableF to view DE genes for a set of contrasts, I am not able
to filter genes based on their log-fold change?
Also, on a related note, under p.adjust argument, in the description
for "BH" method, it said this method controls
Here is the step where I get the error (P. 3 of the waveTiling
"vignette" PDF file):> delta <- log(1.2,2)
> leafdevInfCompare <- wfm.inference(leafdevFit,
+ contrasts="compare",delta=c("median",delta))
The error is:
Error in
updated 11.7 years ago • chris blazier
i have done exprs() call
I am getting negetive value for this
__I have not any fold change or log FC over this data__
Code :-
__setwd("MCF7/data")
cels = list.files("MCF7/data", pattern = ".CEL")
raw.data=ReadAffy(verbose=TRUE
updated 8.2 years ago • kritikamish99
Recent ...
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