div class="preformatted">Hello,
I want to compare two GEO datasets based on the time series data. I
want to
be able to draw some visual highlighting/showing the difference in the
expression of the two sets.
Can
Order by: Relevance
<div class="preformatted">
Hello all!
I am having trouble interpreting whether my SAM outputs are valid
enough
that I should take them seriously, or whether to ignore them and try
another method.
Here is a sample of some of my output (samples are two-class paired
samples; infected cells vs. non-infected cells with 3 different human
donors for the cells; normalized with GCRMA):
Gene set#1…
updated 20.0 years ago • Ettinger, Nicholas
the output files.
How can avoid this problem?
This is the error message
Creating database /data/projects/LL/comp/test_cdout/cuffData.db
Reading Run Info File
/data/projects/LL/comp/test/04_DE/test_cdout/run.info
Writing...runInfo Table
Reading Read Group Info /data/projects/LL/comp/test/04_DE/test_cdout/
read_groups.info
Writing replicates Table
Reading
/data/projects/LL/comp/test/04_DE
updated 13.2 years ago • Estefania
I was trying to download clinical data from the TCGA-KIRC project and it is failing.
I found out it was downloading a TXT file and trying to read it as an XML (id: `` 64a1b6e7-d037-4502-bbad...I was trying to download clinical data from the TCGA-KIRC project and it is failing.
I found out it was downloading a TXT file and trying to read it as an XML (id: `` 64a1b6e7-d037-4502-bbad-0d07849fc32e.…
updated 7.6 years ago • andre.verissimo
design and programming skills, experience in statistical analysis, and the ability to work collaboratively within a team setting. More details may be found at:
<https://morgridge.org/computational-biologist
Hi, so I've been going through some code from a collaborator and I have found bot seqselect and subsetByRanges were removed from IRanges in newer versions. Does anyone
my starting
population. So I have made a targets file that looks like this:
targets
ArrayNames Person Diet Time
1 JALI-173_post 173 Control post
2 JALI-173_pre 173 Control pre
3 JALI-205_post 205 lowFV post
4 JALI-205_pre...263 highFV pre
17 JALI-276_post 276 Control post
18 JALI-276_pre 276 Control pre
then,
person<-factor(targets$Person)
diet&l…
Hello,
I am doing a project for aCGH+SNP analysis. So, I am stuck at a point and need some guidence.
The problem is:
As the project has been done by some...but now it has been updated to Hg19 version.
So, can i procced with the Hg 19 design file for the project or should go for Hg18 design file only.
Need an answer as soon as possible.
Thank you,
Ajay Katoch
updated 10.8 years ago • kajayh
those making significant outstanding contributions to the Bioconductor community. The Bioconductor project proudly launches the first call for Bioconductor Awards, honoring various forms of contributions to the project...Four awardees will be selected, each having contributed to the project in an outstanding way
based on one or more of the criteria found [here](https://docs.google.com/document/d…
updated 5.6 years ago • shepherl
of programmers who otherwise
do not have the opportunity to interact on a routine basis meet to
collaboratively develop working code that is of utility to the
community as a whole. This event will bring together different...benefit.
5. Please indicate if you are a member of an underrepresented group
(including women, persons with disabilities, and any of the
following minorities: African…
updated 18.3 years ago • Hilmar Lapp
377.6957 -330.1110 NaN*
Where does this NaN come from?
Next, I tried to add var2 as the third parameter:
*res1 <- flowClust(mydata, varNames=c("var1", "var2", "var3"), K=1,
B=100)*
*mydata2 <- mydata[mydata %in% res1,]*
*res2 <- flowClust...B=100)*
And again the same error as above. This time it only works with up to
K=1:3, and again the third BIC is NaN. So next tr…
updated 13.8 years ago • Anja Mirenska
I am doing overrepresentation analysis with enrichKEGG.
What I am wondering, is which gene set to use in this situation:
1. I did GWAS and obtained a list of significant variants, and genes linked to them --> first set of genes
2. Then I did fine-mapping of significant variants and narrowed down the number of variants from step 1. and genes linked to them --> second set of genes
…
updated 15 months ago • strawberry3
information you provide us is all non-sensitive and
anonymous. No part of it is handed down to any third party
groups.
It will be stored in our secure database for maximum of 3 days
while we process the results of this nationwide
Hi,
I am using a third party software that uses IRanges package for variant calling. I have a BAM file and there are over 30M reads that are...Hi,
I am using a third party software that uses IRanges package for variant calling. I have a BAM file and there are over 30M reads that are on
updated 9.4 years ago • abolia
Hello,
I use the DESeq2 package for many projects in which the number of samples is quite small. But, sometimes i have some projects with almost 700 samples and i want...to do the same kind of analysis for all the projects.
When the number of samples is huge the estimation of the dispersion is very time consuming. In this specific case
updated 8.2 years ago • stevenn.volant
Dear all,
The Computational Biology group at Illumina Cambridge Ltd, UK, is
offering
six projects for student internships.
The topics of the project are:
- Interactive visualisation of genomic information
- R API...Applications of the Burrows-Wheeler transform to DNA sequence
data
More details regarding each project, the requirements and the
application
process can be found at:
https://…
updated 12.9 years ago • Adrian Alexa
in three backticks as shown below
```BiocManager::install(c("SingleR"))
g++ -std=gnu++17 -I"/project/soft/linux64/R/R-4.2.2/lib64/R/include" -DNDEBUG -I../inst/include/ -I'/project/soft/linux64/R/R-4.2.2/lib64/R/library/Rcpp/include...I'/project/soft/linux64/R/R-4.2.2/lib64/R/library/beachmat/include' -I'/project/soft/linux64/R/R-4.2.2/lib64/R/library/BiocNeighbors...pc-linux-gnu (64-bit)
R…
updated 2.9 years ago • cisbio
I'm trying to do a meta-analysis using the hazard ratios (and their
std
errors) in two independent series. It is the first time I am doing
this, so I
don't know how to proceed.
I think that the package "meta" and its function metagen
updated 16.1 years ago • Antoni Picornell
div class="preformatted">A reference on the titration series have been added to the limma
User's
Guide at
http://bioinf.wehi.edu.au/limma/usersguide.pdf
I worry about spike-in...controls artificially up or down in
the MA
plot relative to the other spots. I find the titration series more
reliable
because it does not require any addition to your experimental samples.
For normalizing with a…
updated 20.3 years ago • Gordon Smyth
To Whom It May Concern,
I have been analyzing two large RNAseq projects separately and successfully. Recently, it was suggested that I merge the analyses so that normalized gene counts
updated 9.3 years ago • arom2
those making significant outstanding contributions to the Bioconductor community. The Bioconductor project is announcing the call for Bioconductor Awards, honoring various forms of contributions to the project. Four awardees...will be selected, each having contributed to the project in an outstanding way based on one or more of selection criteria. More information and details found [here](https:/…
updated 3.8 years ago • shepherl
a geno class object to run snmf analysis:
write.geno(DF2,"srr_wild.geno")
And run the analysis
project = snmf("srr_wild.geno", K = 1:10, entropy = TRUE, repetitions = 10, project = "new",ploidy = 2)
According to the analysis, I selected k...4. Then I ran the following:
p = snmf.pvalues(project,
entropy = TRUE,
ploidy = 2,
K = 4)
I …
those making significant outstanding contributions to the Bioconductor community. The Bioconductor project is announcing the call for Bioconductor Awards, honoring various forms of contributions to the project. Four awardees...will be selected, each having contributed to the project in an outstanding way based on one or more of selection criteria. More information and details found [here](https:/…
updated 2.7 years ago • shepherl
those making significant outstanding contributions to the Bioconductor community. The Bioconductor project is announcing the call for Bioconductor Awards, honoring various forms of contributions to the project. Four awardees...will be selected, each having contributed to the project in an outstanding way based on one or more of selection criteria. More information and details found [here](https:/…
updated 4.8 years ago • shepherl
Dear Bioconductor Community,
I have a workflow for multiple plates single-cell RNASeq that works as follows
1. QC
2. Use RUVSeq to eliminate library complexity bias from data (this works really well, with pre and post)
3. Account for Zero Inflation using Zinbwave
4. Model differential expression using DESeq with model: ~W\_1 + group
I appreciate any comments on this, but this…
into practice.
Topics overview:
? Genomic variation
? Omics-derived biomarkers
? Personal genomes and pharmacy
? Model systems
? Personal health management, economics, ethics
Wolfgang Huber
EMBL
http://www.embl.de
Julia; familiarity with Bioconductor, tidyverse, quarto are a plus
- Enthusiasm for driving a project through all stages of the software development life cycle
- Willingness to engage with cloud computing tools, containerisation...in open source software communities. The interdisciplinary and international team has strong collaborations with researchers in cancer and developmental biology. They u…
updated 11 months ago • Wolfgang Huber
recognition, with the
option to be extended by additional 2 years. This position is part of
a
collaboration program between Philips Research Eindhoven, Sector
Molecular Medicine and UfAS Wildau, Dept. Bioinformatics...he is able
to take over teaching duties in case of absence of the dept. head and
supports him in project management and acquisition. We expect that the
candidate is interested in ex…
updated 16.7 years ago • Paul Hammer
for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages
updated 15.6 years ago • Jennifer Ehren
for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages
for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages
updated 16.3 years ago • Ross Lazarus
Dear Community,
for an ongoing collaborative project, i want to analyze a transcriptomic dataset, which is not deposited in GEO, but in ArrayExpress:
__https
updated 7.3 years ago • svlachavas
for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages
for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages
updated 9.9 years ago • raf4
<div class="preformatted">Dear list,
Here is a job announcement from M.D. Anderson. Interested applicants
should contact Susan L. Tucker, Ph.D., Head of the Faculty Search
Committee, at sltucker at mdanderson.org.
The Department of Bioinformatics & Computational Biology (DBCB) at The
University of Texas M. D. Anderson Cancer Center is seeking candidates
for available faculty posit…
<div class="preformatted">Hi,
I am trying to work with GEO dataset GSE2180, containing time-series
experiments including 10 time points for 4
different genotypes. The files include the .CEL and .EXP, these last
ones containing...div class="preformatted">Hi,
I am trying to work with GEO dataset GSE2180, containing time-series
experiments including 10 time points for 4
different genotypes.…
updated 19.9 years ago • LUIS F MENEZES
div class="preformatted">hello eveybody,
I'd like to know your opinion about how to analyze time-serie
experiments with BioC.
We use a common reference (gDNA) at each time point.
According to you wich is the simplest method
updated 21.6 years ago • marchiem@libero.it
Hello,
I now need to generate a Bsgenome that is a fusion genome of a person and the HIV-1 virus. I already have the fa files of hg38 and HIV-1 from NCBI. I keep getting errors when running the seed...Hello,
I now need to generate a Bsgenome that is a fusion genome of a person and the HIV-1 virus. I already have the fa files of hg38 and HIV-1 from NCBI. I keep getting errors when running th…
updated 2.2 years ago • 13273976287
Bioconductor community! Deadline: **this Wed May 31 23.59 ET**
- Early reg & in-person scholarships for BioC2023:
[https://bioc2023.bioconductor.org/registration/][1]
- BioC Award nominations: [https://support.bioconductor.org
updated 2.6 years ago • Maria Doyle
Hi All,
Firstly I have very little experience in R (I am a wet lab person); so if this is not the correct forum for this question please ignore it. I am using Gviz to plot transcripts from 5 different
updated 5.6 years ago • peris_baba
those making significant outstanding contributions to the Bioconductor community. The Bioconductor project is announcing the call for Bioconductor Awards, honoring various forms of contributions to the project. Four awardees...will be selected, each having contributed to the project in an outstanding way based on one or more of selection criteria. More information and details See [BiocAwards Webs…
updated 23 months ago • shepherl
<div class="preformatted">Hi all,
I am completely new to the analysis of Illumina Beadarray gene
expression data (but quite familiar with Affy data). Such data (with
samples run on 3 chips) was sent to me by a collaborator. From the
vignettes for Bioconductor packages 'beadarray' and 'BeadExplorer', it
looks like these accommodate Beadstudio version 1 and 2 data, while
our
data was cr…
My gtf file seems to have the 9 columns specified by the
gtf format when looking at it in a text editor, but on import I have 9
columns labeled as "X1.", "X2",...,"X9." nearly all of the entries are
NA. In X1. there are 817 "1\" entries (of 474351
updated 12.8 years ago • Guest User
Dear Bioconductor community,
based on a current project aiming to decipher prognostic biomarkers that driving the response to chemotherapy in breast cancer, we are trying
updated 4.5 years ago • svlachavas
features and
principles of the spatiotemporal dynamics of biological development.
The project will be carried out within the Computational Biology
Laboratory at the School of Computing Sciences. Co-operation...unique opportunities for
validating and improving your models using empirical data.
Working on this project requires skills / experience in (1) computer
models of complex biological syste…
I have a chip-seq data set with three conditions (wt , KO1, KO2) and three time points (0h, 2h, 4h). For each condition and TP I have duplicated samples for IP and Input samples, which looks like that:
<table border="0" cellpadding="0" cellspacing="0" style="width:235px">
<tbody>
<tr>
<td><strong>condition</strong></td>
<td><strong>TP</str…
updated 8.2 years ago • Assa Yeroslaviz
source("http://www.bioconductor.org/biocLite.R") ``
* `` biocLite() ``
* `` created a personal library since I didn't start RStudio as sudo. ``
* `` biocLite("AnnotationHub") (personal library again, update all old packages
updated 9.7 years ago • barashe
Greetings,
I have a sample with four different conditions:
1uE, 10 uE, 100uE, 500uE
The conditions are analyzed as pairs:
1uE vs10 uE
1uE vs 100 uE
1uE vs 500uE
Using the examples in the DESeq tutorial it appears that I would have
to
analyze these pairs as having no replicates but I'm thinking I really
have
four replicates. Is there a way to calculate the dispersion using all
of
the data and t…
Hello, Here is lot of about RNA-Seq time course experiments so I have chaos. If is somewhere correct answer for me, please send me link.
I have time course experiment - 3 condition - 1 control + 2 treated, and 4 times
LibraryName countf condition time 1 WT-0-mpw-B WT-0-mpw-B_union.count WT 0 2 WT-0-mpw-D WT-0-mpw-D_union.count WT …
updated 9.6 years ago • pavel.abaffy
Hi,
I am writing to clarify on the design matrix for running edgeR on data with multiple time points with two conditions.
condition time Group
sample1 condition1 T0 c1.to
sample2 condition2 T0 c2.t0
sample3 condition1 T1 c1.t1
sample4 condition2 T1 c2.t1
sample5 condition1 T2 c1.t2
sample6 condition2 T2 c2.t2
Following section 3,3 in the edgeR manual, to find different…
updated 7.0 years ago • sharvari gujja
Hello,
I am working on 2 isogenic cell lines which are treated with a
certain chemical and 24h, 48h, and 72 hour samples are taken. We now
have 12 arrays (4x 3 time points) and its duplicate. I searched for
some methods for the analysis of this kind of data, yet I could not
find one.
Could you please advise me the most convenient R package and
statistical method to perform such an analysis...
…
updated 18.9 years ago • Ozge Gursoy-Yuzugulu
Hi Ozge,
I would recommend you to have a look at the simpleaffy package from
Crispin J Miller.
http://bioconductor.org/packages/1.9/bioc/html/simpleaffy.html
The vignette pdf explain how to extract genes significantly regulated
when you have replicate in you experiment.
David
---
David RUAU
Institute for Biomedical Engineering
-Cell Biology-
Universitatsklinikum Aachen, RWTH
Pauwelsstrasse 30…
updated 18.9 years ago • David Ruau
edgeR from source, I am getting the following error messages :
a. shall I setup .libPaths() to a personal folder only :
.libPaths("/Users/tanasab/Desktop/SOFTWARE/R")
the error message is :
The downloaded source packages are...Versions/4.2-arm64/Resources/library
b. OK, it is expected, but shall I setup .libPaths() to a personal folder + OS folders,
.libPaths(c("/…
updated 3.3 years ago • Bogdan
in computational biology
Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists
Strong oral and written communication, data documentation, and presentation skills...Excellent collaborative and interpersonal skills.
DEADLINE & REQUIRED APPLICATION MATERIALS
Applications for Summer 2022 internships...biology research?
…
updated 4.1 years ago • simonsF.careers
base=2)
Is there any reason why we should use one or the other? or is just a matter of personal likes?
Thanks
Catalina
 
GSE2466_family.soft.gz'
where we
had to use both the
Affymetrix HGU95A and HGU95Av2 chips. In my personal opinion it is a
serious
flaw of the GEO
database that it declares both chips as single platform GPL91.
In your description...created: 01/19/2006 last modified:
01/19/2006
# Get sample table of columns "column" for GEO Series GSExxxx
# gse: GEOqueryclass imported from GEO GSE file GSExxxx…
Hey!
Thank you for a great resource! I am learning how to use DESEQ2 on time-series and I would like to get advice if my analysis is statistically "correct".
I have a single time-series i.e. the first time
updated 3.3 years ago • Jigyasa
I'm running a series of linear regressions on a subset of candidate genes using `` lmFit(.) `` from the limma package. Two, hopefully simple questions...create a matrix of residuals controlling for another factor (sex) so I can look at the effects of a series of variables in a loop. Does it still make sense to use the `` fit <-eBayes(fit) ``, as I've seen recommended?
I ask because I don
updated 9.5 years ago • CPR
ChAMP.
ChAMP is a integrated DNA methylation analysis pipeline, the new feature of ChAMP included a series of GUI function for user to check and generate interactive plot for DMP, DMR, DMB... This series of function used shiny and
<div class="preformatted">On Tue, Oct 12, 2010 at 4:51 AM, Georgia Tsiliki
<g_tsiliki@hotmail.com>wrote:
> Dear Dr Davis,
> I am a biostatistician at BRFAA, Athens. I am currently using the
> 'GEOquery' package with Bioconductor/R. I had a problem with GSE3494
series;
> particularly, i cannot download the 'Data Table of the
Clinicopathological
> va…
Recent ...
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Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
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JKim
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0
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He left some comments regarding normalization. Here is the relevant quote:
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James W. MacDonald
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jason.chai
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Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Comment: Questions about bacon QC and correction on EWAS results
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This is qq plot and histogram generated before bacon correction
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