Bioconductor Forum

Hi, I am working with time-series mice serum lipidomics data, and would like to make sure I have the right design for my purpose. The experiments like...Hi, I am working with time-series mice serum lipidomics data, and would like to make sure I have the right design for my purpose. The experiments like: Using...8 days respectively after exposure. I read some articles about soft clus…

mfuzz normalization

updated 6.5 years ago • xizhang

<div class="preformatted">i have 5 time points of expression data, i would like to do some clustering or other time series analysis. thank you -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute for Plant Research Cornell University Tower...i have 5 time points of expression data, i would like to do some clustering or other time series analysis. thank you -- shan gao Room 231(Dr.Fei…

Clustering Clustering

updated 12.4 years ago • wang peter

<div class="preformatted">Hello, I have two questions concerning the same data set. I have a number of time series data (say, S1 - S10). Each time series consists of a few time points (T1-T5), without replicates (you play what you are dealt...). First question: there is a hypothesis that one of the time series stands out in respect to a number of genes. The goal would be to find these gen…

updated 15.0 years ago • January Weiner

all I'm trying to execute the code in the working paper "Differential expression with bioconductor project". I obtain a null vector when use the instruction: esetSub$mol=="BCR/ABL" is it correct? Thanks in advance! </div

updated 20.3 years ago • fede@dssm.unipa.it

clinical study of patients treated with BsAbs. This work takes place within the Transcan-3 project Bispecific antibodies in Lymphoma: Microenvironmental profiling to predict treatment response and uncover...resistance mechanisms (BIALYMP). This international collaboration combines biotechnological and computational research groups with clinical oncologists and is coordinated...to develop new biom…

omics Spatial postdoc

updated 2.8 years ago • Wolfgang Huber

data science, and data visualization. All students are expected to complete a capstone research project and to participate in a seminar series.   The MBI Curriculum Fellow will play a key role in developing the educational...associated teaching faculty. * Take a lead role in planning and mentoring the capstone research projects. * Work with the MBI Director and faculty to expand th…

biomedical informatics data science Job

updated 7.7 years ago • Doe, Aimee

hgu133plus2. The other used a combination of hgu133plus and hgu133plus2 arrays. Specifically, two thirds of the arrays were hibridized on hgu133plus and one third was hibridized with hgu133plus2. I would like to combine...comparisons that were performed and then I would like to compare it with the newest one. One of my collaborators performed RMA separately on the two sets of chips and then merge…

Normalization hgu133plus2 Normalization hgu133plus2

updated 17.0 years ago • Alex Sanchez

I have a series of genomic ranges accompanied with metadata. For example, the simplest case is: Chromosome Start End Score chr1 1234567...reduced to: chr1 1234560 1234940 50 chr2 1234560 1234940 50 .. since the first 3 overlap and the third is the one with the highest score, while the last three also overlap and the 6th has the highest score. Any ideas? &nbsp

genomicranges

updated 9.9 years ago • IV

Science function exists to ensure effective strategic Translational Science Biomarker input into project teams. Closely interacting with iScience, functions and collaborators, iMed Translational Science will develop...the single point of accountability for delivery of robust, scientifically-driven biomarkers in all projects. The Translational Genomics Scientist role will be a key driver of biomar…

cancer translation ngs genomics Job

updated 10.8 years ago • jhjohnsn

div class="preformatted">Student Intern Project, Summer 2007, Chicago, IL Although undergraduates are welcome, masters and PhDs in computational biology are preferrered...of Northwestern University, downtown Chicago. For details, see http://www.basic.northwestern.edu/projects/SoC07/index.html Depending on the project and personal interests, programming skills in R/Bioconductor/Java/Python

Cancer Cancer

updated 18.8 years ago • Simon Lin

and causal inference method development for analysis of large genomic datasets. The goal of this project is to develop mechanistic understandings of genetic risk for neuropsychiatric disorders as mediated through...and disease phenotypes). The work will connect closely with multiple international groups via active collaborations, and seek to maximize impact through open source software release, a…

postdoc Job

updated 5.9 years ago • Michael Love

div class="preformatted">Hi, all, Has anybody done cross experiments or GEO series normalization on Affymetrix arrays? Any suggestions or related links will be highly appreciated. Thanks, Chuming

Normalization Normalization

updated 20.5 years ago • Chuming Chen

div class="preformatted">Hello All I'm having difficulties carrying out a time series analysis of my dataset using Bioconductor! Could anyone help me out in this area: I have microarray time course data...with E B with E C with E and D with E Using BH method in LIMMA analysis how do I carry out a time series analysis of this time course data? Any useful suggestions in the area of matrix desi…

Microarray limma Microarray limma

updated 17.5 years ago • yemi yomi

spatial) proteomics, post-translational modification and machine learning. The goal of the project is to apply and extend existing spatial proteomics methods ([1][2], [2][3], [3][4]) and software infrastructure (such as the [pRoloc...proteoform sub-cellular localisation. This position is part of the FWO-funded Protein Contours project, in collaboration with Win Vranken from the VUB and Lenn…

pRoloc proteomics Spatial Proteomics MassSpectrometry

updated 2.9 years ago • Laurent Gatto

computational biology, or closely related area. Additionally, applicants should have collaborative research experience. Primary responsibilities include teaching and advising graduate students as well...independent methodological research. In addition, the successful applicant will be expected to collaborate with other VCU investigators in related fields in obtaining extramural gr…

Sequencing Cancer Sequencing Cancer

updated 13.3 years ago • Kellie J. Archer, Ph.D.

including microarray and next generation sequencing technologies. The Bioinformatician will collaborate with individual lab members on customized research projects, and work on independent projects that are solely...br/> * Integrate computational methods/pipelines with high performance computing clusters<br/> * Collaborate closely with PIs and their lab members on research …

Bioinformatician Job

updated 11.2 years ago • Julie Zhu

div class="preformatted">Dear Web Master: *I want to unsuscribe from The Bioconductor Project Mailing List.* *Thanks* [[alternative HTML version deleted]] </div

updated 13.9 years ago • Maximiliano Sánchez Lamas

Aspects of Microarray Analysis (V) 18-22-June-2007, Bressanone-Brixen, Italy This 5 days lecture series provides an introduction to genomic data and their interpretation. The main focus will be on microarray experiments...Munchen, (D) The course is organized jointly by Universities of Milan and Padua, Italy in collaboration with the Biocondutor project and the R Foundation for Statistical Compu…

Microarray Proteomics Preprocessing Cancer Microarray Proteomics Preprocessing Cancer

updated 19.0 years ago • stefano iacus

<div class="preformatted">Hi: Are there any ways or algorithms to carry out a meta-analysis of time series gene expression data sets. I know it is not an appropriate analysis since timepoints may not be comparable across experiments...div class="preformatted">Hi: Are there any ways or algorithms to carry out a meta-analysis of time series gene expression data sets. I know it is not an ap…

updated 13.0 years ago • Adrian Johnson

class="preformatted">Dear Prof Smith, dear Bioconductor's user, I am using Limma to analyse time series microarray gene expression data. I have 4 time points (t1: 40 RNAs, t2:42, t3:20,t4:30). RNAs are isolated from 42 patients. could

Microarray limma Microarray limma

updated 16.6 years ago • claire pujoll

was wondering if anyone could give me pointers for the following situation. Given a time course data series with 3-4 repeats for individual time points, what is the best way of determining a list of differentially expressed

updated 18.6 years ago • peter robinson

and that the edgeR Users Guide would contain coded examples. Alas, I cannot find anything on time series there. Has anyone addressed 'my' situation? If so, I would appreciate being notified. best regards jahn -- output of sessionInfo

edgeR edgeR

updated 12.1 years ago • Guest User

The [Gottardo Lab][1] at Fred Hutch is a research lab within the computational biology program focused on creating statistical methods and software tools to analyze high throughput biological data. In collaboration with bench scientists and clinicians we work to understand severe diseases such HIV, malaria, and cancer and...on creating statistical methods and software tools to analyze high throug…

SEATTLE WASHINGTON STATE WASHINGTON BIOINFORMATICS Job

updated 5.8 years ago • Fred Hutch (Recruiting)

will join the research group of Professor Laurent Gatto and will have the opportunity to work on projects across a broad range of biomedically relevant topics in collaboration with researchers of the biomedical campus...software engineer will be expected to contribute to various activities, including : - Research projects: support and advise collaborators with their data analyses and contribut…

software engineer RNASeq proteomics Job visualisation

updated 5.6 years ago • Laurent Gatto

<div class="preformatted"> Hi Mette, > We have one-color ABI-data from 3 persons at 2 timepoints (a pilot > study), and want to compare the gene expression at the two timepoints > for a group of genes. > We could forget that the same person gave rise to two correlated values > in time and run globaltest with y=0,0,0 for the samples at timepoint 1 &gt…

globaltest globaltest

updated 19.3 years ago • Goeman, J.J. MSTAT

Hi, I'm trying to use GEOquery's getGEO for downloading the series matrix file of several studies using their `` GEO `` accessions, from my linux cluster. I originally tried: geo.accession...out.dir)</code>   And this is the output I get: <pre> https://ftp.ncbi.nlm.nih.gov/geo/series/GSE11nnn/GSE11675/matrix/ OK Found 2 file(s) /geo/serie…

GEOquery getGEO

updated 7.8 years ago • rubi

in a single study, but rather in analysing multiple datasets together. For example: ```r projects <- c("SRP009615", "SRP013565") proj_info <- subset( human_projects, project %in% c(projects) & project_type == "data_sources...proj_info project organism file_source project_home project_type n_samples 33 SRP013565 human sra data_sources/sra dat…

recount3 recountWorkflow

updated 4.3 years ago • António Miguel de Jesus Domingues

div class="preformatted">Hi, I wonder how to analyze a RNA-Seq dataset of a time-series experiment. The dataset origin from a challenge experiment with 4-6 samples per time point (T00,T06,T12,T24 and T48) from...two series of challenge (with one of two different serotypes). In total 48 individual samples and two factors, time and serotype...lattice_0.19-13 limma_3.6.6 svMisc_0.9-60 tools_2…

Genetics edgeR Genetics edgeR

updated 15.2 years ago • Jakob Hedegaard

<div class="preformatted">Hi all. I am a community college student in Arizona and I'm enrolled in an introductory level bioinformatics course. As part of the requirements, I need to submit a course project of my own choosing/design. I am very interested in looking at the BRCA1, BRCA2, and Errb2/neu genes for evolutionary similarity...an introductory level bioinformatics course. As part of …

updated 13.2 years ago • Caitlin

a bioinformatician/statistician with interest in the application. If interested, please contact the project leaders as indicated below and not me. _________________________________________________________ The department...of psychiatry and biological psychology of the VU University Medical Center and VU University collaborate in a large- scale study into the genetics of major depressive disorde…

Genetics Genetics

updated 15.9 years ago • Menezes, R.

people willing to share their knowledge and eager to learn from each other. You will work in a collaborative and nurturing environment that values diversity, personal development and integrity. We believe that diverse...deploy interactive shiny apps for visualization of results from our Disease Cancelling Technology • Collaborate with colleagues to develop analysis methods and algorithms to sol…

bioinformatics rna-seq shiny apps R algorithm development Job

updated 5.2 years ago • mmartin

will join the research group of Professor Laurent Gatto and will have the opportunity to work on projects across a broad range of biomedically relevant topics in collaboration with researchers from the de Duve institute...software engineer will be expected to contribute to various activities, including : * Research projects: support and advise collaborators with their data analyses and contrib…

software engineer job teaching bioconductor Job

updated 7.2 years ago • Laurent Gatto

quick question for you, not sure if you are able to help if not can you point me towards the correct person. I am following this tutorial: [Group-specific condition effects, individuals nested within groups][1] and I understand...plots so following the tutorial I added a dummy based on the subplot, but since this is also a time series, do I need to add a dummy for Plot since I have multiples …

deseq2 edger

updated 5.8 years ago • mpuli011

I will be grateful for your feedback and advice. I have been tenured for some time now and appreciate that my statistics training was very different than what is available now. Can I use WGCNA to identify clusters of responsive proteins from one perturbation time series (pooled from two independent replicates)? I plan on following up with additional proteomic experiments, based on specific c…

WGCNA

updated 2.7 years ago • Adam

team featuring programmers, computational biologists and bench scientists, senior analysts work collaboratively for extended periods with other research groups within the Institute, where they are able to bring their...expertise in genomics analysis to multiple projects and datasets. Senior Computational Biologist Reference number: PI/12/57 Starting salary: range: ?33,300 to ?57,100 (dependent.…

Sequencing Cancer Sequencing Cancer

updated 13.1 years ago • Crispin Miller

potential. Flexibility and the ability to work in a multidisciplinary environment and on parallel projects are essential. We offer an open and stimulating scientific environment, a range of exciting projects and state of

Proteomics Proteomics

updated 13.7 years ago • Amin Moghaddasi

Dear all, my time series experiment; I exposed my plant to light and harvest after 6 time points (0, 0.5, 2, 4. 8, 10h), therefore, I have the effect of the...Dear all, my time series experiment; I exposed my plant to light and harvest after 6 time points (0, 0.5, 2, 4. 8, 10h), therefore, I have the effect of the conditions  (light), the Time, and the interaction (ligh…

deseq2 tximport

updated 7.1 years ago • ahmedaalkarim

Medical Center. A successful candidate is expected to pursue methodological research and work on collaborative biomedical projects. The laboratory is involved in various externally funded methodological and collaborative...biomedical research projects and activities ranging from analysis of next-gen sequencing data to developing novel statistical/machine learning

Sequencing Microarray Sequencing Microarray

updated 14.2 years ago • Medvedovic, Mario medvedm

Levels: Control1 Control4 Treatment1 Treatment4 ? I saw that most guides on time series report >=3 time points, so another question is: can I use a "time series" workflow with just two time points? Thank you all

DESeq2

updated 3.8 years ago • Francesco

to immunology. The position is located in the Biostatistics unit (head: Daniel Commenges, former editor of Biometrics) in Bordeaux (France) with a strong collaboration with Prof Yves Levy?s team (Henri Mondor, Paris, France...in addition to antiretroviral treatment. The position requires the availability to visit collaborators in United States at the Baylor Institute and other relevant teams to l…

Cancer Cancer

updated 15.3 years ago • Audrey Kauffmann

Hi, I have time-series data (in order to measure the half-life of RNA degradation) under different conditions. To test any genes react in a condition...experiments Alternatively, I could also calculate the half-life of each gene based on their time-series normalized expression values (like the [HalfLivesBlock()][1] in DRUID code) and then model the half-life (instead of gene...dispersion (…

half-life DESeq2 time-series

updated 4.7 years ago • Xianjun Dong

Two positions available at CUNY SPH working with myself and Nicola Segata (University of Trento) to understand roles of the microbiome in Parkinson's Disease, in collaboration with the Michael J Fox Foundation ASAP network. Includes competitive pay $75-85K/yr, conference travel, and 1 mo/yr at @cibiocm in Italy. In-person or remote work possible. To be filled ASAP. 1. Postdoc: [https://www.rf…

Metagenomics curatedMetagenomicData bugsigdbr

updated 2.0 years ago • Levi Waldron

Lana, The MSigDB is a good source! We are planning to have a summer student working on a similar project, but using a different database. Maybe we can coordinate the efforts. Simon Message: 4 Date: Mon, 12 Mar 2007 14:39:54 -0700

Category Category

updated 18.8 years ago • Simon Lin

Job Posting #914878 Position: Bioinformatics Analyst Site: Princess Margaret Cancer Centre Department: Medical Oncology and Hematology Reports to: Principal Investigator Hours: 37.5 per week Status: Permanent Full-time University Health Network (UHN) is looking for an experienced professional to fill the key role of Bioinformatics Analyst in the Medical Oncology and Hem…

bioinformatics ngsReports NGS analyst science

updated 2.9 years ago • marisona.almazan

with experience working on computational analysis of biological data, and who are interested in project organisation and management. The positions involve extensive collaboration with scientists across EMBL. Their...researchers, organising events, creating and maintaining related web resources, and participating in collaborative research projects. 3. Biostatistician: Centre for Statistical Data …

Sequencing Network Sequencing Network

updated 13.4 years ago • Wolfgang Huber

please visit: http://www.economia.unimi.it/ marray Description follows: This 5 days lecture series provides an introduction to genomic data and their interpretation. The main focus will be on microarray experiments...Munchen, (D) The course is organized jointly by Universities of Milan and Padua, Italy in collaboration with the Biocondutor project and the R Foundation for Statistical Computi…

Microarray Proteomics Preprocessing Cancer Microarray Proteomics Preprocessing Cancer

updated 18.7 years ago • stefano iacus

div class="preformatted">dear group, What are the GO analysis methods for time series data analysis. experiment: 50 samples (cell line) treated with drug 4 time points (2hr, 4hr, 8hr, 24hr) Once the clusters of

GO GO

updated 18.2 years ago • Srinivas Iyyer

preparation for on-going and future research projects.  This position will have ample opportunities for co-authorship and other documentable career-enhancing...A critical, independent, and creative thinker. * A professional, personable, organized individual with research experience in the academic setting. * Excellent oral and written communica…

genetic epidemiology cancer genomics computational biology biostatistics moffitt cancer center Job

updated 7.9 years ago • claudia.lopez-matamoros

<a name="OLE_LINK2"></a><a name="OLE_LINK1">A postdoctoral position is available in the Schizophrenia Center at the Johns Hopkins School of Medicine. The center seeks a talented and highly motivated Bioinformatician/Biostatistician to pursue translational/clinical research projects, including a) first episode psychosis project, and b) chronic schizophrenia and mood disorder proj…

rnaseq next-generation sequencing database Job

updated 8.1 years ago • cleo.k.yang

gt; To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Analysis: two-color, time series > Content-Type: text/plain > > Dear List, > > I need help with the analysis of time series experiment. I have cDNA &gt

Microarray limma Microarray limma

updated 15.4 years ago • Gordon Smyth

Similar as this question:** https://stats.stackexchange.com/questions/2592/how-to-project-a-new-vector-onto-pca-space Simple question. How would we project a new vector onto PCA space using **snpgdsPCA( )**, given

SNPRelate

updated 3.8 years ago • MatthaeusCaesar

data sources to identify key drivers of disease Research The successful applicants will work on collaborative projects in breast cancer genetics and genomics, which aim to identify key drivers of disease by integrating...reconstruction of gene networks and diagnosis of disrupted signaling pathways in tumors. The projects will be in close collaboration with the Ponder and Caldas research groups a…

SNP Genetics Pathways Cancer CGH microRNA SNP Genetics Pathways Cancer CGH microRNA

updated 17.3 years ago • Florian Markowetz

<div class="preformatted">Dear All, I would like to analyze a time-series microarray data generated with Yeast 2.0 chip. There are 30 time-points with no replication. Is there any package I could...div class="preformatted">Dear All, I would like to analyze a time-series microarray data generated with Yeast 2.0 chip. There are 30 time-points with no replication. Is there any package…

Microarray Microarray

updated 17.0 years ago • Paco Recca

div class="preformatted">Just an FYI, NCBI GEO is having some trouble with Series Matrix files (since yesterday), so getGEO() with a GSE will likely fail right now. The GEO folks are working to fix the problem

updated 15.5 years ago • Sean Davis

informatics resources; test the clinical validity of those items with likely impact in the personal medicine clinical enterprise; and to execute high priority projects that translate key technologies into the...clinical IT enterprise in support of LPM’s healthcare collaborator’s strategic personalized preventive medicine objectives.  The long-term goal is to create a translational...s so…

software engineer bioinformatician job Job

updated 11.2 years ago • Doe, Aimee

div class="preformatted">Hi BioC users and contributors, In order to improve collaboration between scientists, computer engineers, bioinformaticians working with R and Bioconductor, I would like...in the list, would be interested in developing or making part of a website that plays the role of collaborative platform for R/Bioconductor codes, packages, workflows and contributions, so that we d…

updated 15.1 years ago • Radhouane Aniba

Dear Gordon, I am referring to the RNAseq123 workflow section [8.7][1]: For these sorts of time-series experiments for which we assume a certain pattern (circadian for example), wouldn't it make sense to also calculate...Dear Gordon, I am referring to the RNAseq123 workflow section [8.7][1]: For these sorts of time-series experiments for which we assume a certain pattern (circadian for example)…

limma

updated 3.1 years ago • ATpoint

I am trying to use GEOquery to download the data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39133. Based on the [vignette](https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html#overview-of-geo), I should be able to just run the code: <pre> gse <- getGEO('GSE39133')</pre> This produces the following output: <pre> ftp:…

geoquery ncbi geo geo data

updated 9.2 years ago • fongchunchan

I have manually downloaded a series matrix file from GEO database in my machine. I wish to load this file in R Bioconductor. What command should I use? <span

geoquery

updated 10.5 years ago • ayanava18

Job Posting #914879 Position: Bioinformatics Specialist Site: Princess Margaret Cancer Centre Department: Medical Oncology and Hematology Reports to: Principal Investigator Hours: 37.5 per week Status: Permanent Full-time University Health Network (UHN) is looking for an experienced professional to fill the key role of Bioinformatics Specialist in the Division of Medical…

bioinformaticsspecialist ngsbasedassays statisticalmodels ngsdataanalysis differentialgeneexpression

updated 2.9 years ago • marisona.almazan