Bioconductor Forum

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JobPosting CuratedAtlasQueryR tidySpatialExperiment tidyomics tidySingleCellExperiment

updated 19 months ago • Stefano Mangiola

more sophisticated I can do with DESeq2 than just applying a mean count cutoff to define the third class? Maybe use the LFC thresholds in some way

DESeq2 deseq

updated 4.0 years ago • penny.lane

what are these values?? I need to know their column headers. first: chromosome second: positions third: strand fourth/fifth/sixth: methylC/UnmethylC/readcount/count of C or T/ count of A or G ????? Chr1 109 + 16 1 1 Chr1 114 + 10 11 1 Chr1

segmentSeq

updated 2.9 years ago • Poonam

<div class="preformatted">Thanks, Michael. That was the tip I was looking for. For what it's worth, neither args (ranges) nor ?ranges led me to the answer you so quickly provided. I spent more than a little time looking. I am a little timid about this -- I thought I already knew how to obtain answers of this sort :} -- but how exactly could I have found out this on my own? If…

updated 16.6 years ago • Paul Shannon

Hello all, I am working on microarray data from GEO (GSE15919). The expression values given in the series matrix file are log2(Cy5/Cy3). I use its platform data (GPL1528) a R package "Annotationdbi" to annotate probes to be an entrez

microarray annotation

updated 7.0 years ago • KCLiv

However, there was a large space of time between the first run and the consequent second and third run (both run at the same time), so I would like to conduct a batch effect. My data set looks something like this: ```` Sample | Biological...In the tech repeats, 1 was the technical repeat run first, and 2 represents the second and third repeat that were run at the same time. The model matr…

MassSpectrometryData BatchEffect r limma

updated 3.5 years ago • mfaleevs

classes for copy number estimates and confidence scores, genotype calls and confidence scores, and a third class that contains both copy number and genotype calls. This third class inherits methods from the other two. We hope

SNP Annotation Yeast Biobase SNPchip SNP Annotation Yeast Biobase SNPchip

updated 19.2 years ago • Justin Borevitz

<div class="preformatted">Dear all, I use BioConductor affy package on a Mac OS X 10.4 machine, ReadAffy crashes R. The same problem has been reported earlier by another user (see http://thread.gmane.org/gmane.science.biology.informatics.conduct or/16747), but no solution has been suggested yet. Here I show you the error message, session and debug information for R 2.7.1, but the same prob…

affy BUS affy BUS

updated 17.5 years ago • Luo Weijun

Just a heads up that some deadlines for BioC2024 are approaching! Take note: - In-person Scholarships: Apply by May 15: [Scholarship Application][1] - BioC Award Nominations: Nominate by May 15: [More details and

BioC2024 Bioconductor Community

updated 20 months ago • Maria Doyle

119, Issue 28" sent on 28.1.13 12:00:04. This is the only notification you will receive while this person is away. ---------------------------------------------------------------------- ---- This email and any files transmitted with it are confide...{{dropped:9}} </div

updated 13.0 years ago • Pie.Mueller@unibas.ch

div class="preformatted"> Get paid US$1-US$26 for answering surveys, Get paid US$1.25 per person you referred to this site. Get paid US$6 the moment you join the survey site. I did not believe it at first, so I tried. They

updated 18.4 years ago • Lee

CEL data: Data<-ReadAffy("a.CEL") But I couldn't read the data in for one case, and the data person told me that it is because the data was created using new expression scanner. Would you please let me know if you have

affy affy

updated 21.6 years ago • Feng He

120, Issue 9" sent on 9.2.13 12:00:03. This is the only notification you will receive while this person is away. ---------------------------------------------------------------------- ---- This email and any files transmitted with it are confide...{{dropped:9}} </div

updated 12.9 years ago • Pie.Mueller@unibas.ch

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

arrayQualityMetrics arrayQualityMetrics

updated 14.1 years ago • Vladimir Zhurov

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

probe gcrma probe gcrma

updated 14.3 years ago • Yupu Liang

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

software error

updated 10.7 years ago • ori.staszewski

it under certain conditions. Type `license()' or `licence()' for distribution details. R is a collaborative project with many contributors. Type `contributors()' for more information. Type `demo()' for some demos, `help()' for

affy affy

updated 22.7 years ago • Duhaime Johanne

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

graphite

updated 7.2 years ago • Lluís Revilla Sancho

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

cummerbund readcufflinks

updated 8.5 years ago • tommy.vo

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 11.7 years ago • Yue Li

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

EBImage BiocInstaller EBImage BiocInstaller

updated 13.5 years ago • Guest User

on the selection of genes and their associated signatures for biomarker pattern development. This project is being coordinated by FDA as a followup to the MicroArray Quality Control (MAQC) Project. This evaluation process...is open to the public. DATES: Datasets and proposals for participation in the project must be received by the National Center for Toxicological Research on or before 4:30 p.…

Microarray Pharmacogenomics PROcess Microarray Pharmacogenomics PROcess

updated 19.7 years ago • Wolfgang Huber

Hey! I want to use the package ‘TMixClust’ for analysing time series expression patterns. Do you have any recommendations on how to import data from DESeq2 into TMixClust? I could not...Hey! I want to use the package ‘TMixClust’ for analysing time series expression patterns. Do you have any recommendations on how to import data from DESeq2 into TMixClust? I could not find

TMixClust time series expression analysis

updated 5.9 years ago • kathrin.garschall

For example "212094_at" does not appear cColor(?212094_at?, "green", newChrClass). I will attach a series of AffyIDS with there Nucleotide positions.</div

hgu133a hgu133a

updated 21.3 years ago • Auer Michael

Hi I'm using DESeq2 to analyze raw read counts. I have 5 groups and 3 batches (different projects). In order to find out which genes are expressed differentially in all groups and also adjust for batch effects I...Hi I'm using DESeq2 to analyze raw read counts. I have 5 groups and 3 batches (different projects). In order to find out which genes are expressed differentially in all groups a…

DESeq2 DEG ANOVA Batch effect Comparison

updated 6.4 years ago • amin.ghareyazi

lapply(dir(fcs_path, full.names = TRUE), read.FCS, truncate_max_range = FALSE) ``` I know that the third frame in this list is the single colored control for CD3, so I pull that frame from the list: ```r CD3_frame <- frames[[3]] ``` This

flowCore flowDensity

updated 3.8 years ago • nmchavez

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factor analysis mofa Job

updated 7.0 years ago • Wolfgang Huber

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…

Recognition Awards Bioconductor Bioc204

updated 20 months ago • shepherl

problem is that data is only available for about half the members of this family. There is only one person where the data of both father and mother is available. Any suggestions on how to analyze this kind of data would be very

SNP SNP

updated 19.1 years ago • Theresa Scharl

Embed scale bar. Is this possible to do in R ? with regards Sundar The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. [[alternative HTML version deleted]] </div

updated 16.2 years ago • sundar Venkat

REBIT-POD postdoctoral fellowships are available to carry out research projects between a laboratory at IIT (Italy) and a laboratory at either EMBL Rome or EMBL-EBI (UK), including a project on Nanopore

nanopore job EMBL IIT Job

updated 6.6 years ago • mattia pelizzola

Hello, I need to use DESeq2 for a series of simulations on a high-performance computing cluster, but the most recent version of R available is 4.0.3. This means

DESeq2 BiocVersion

updated 4.6 years ago • Daisy

div class="preformatted">Hi, I am trying to estimate the spatial correlation for a series of arrays. My design encompasses 9 separate groups (4-5 technical reps per group), and each array has each gene spotted

updated 22.0 years ago • Simon Melov

div class="preformatted">The limma package has now forked into two series, one which depends on R 1.9.0 and one which depends on R 1.7.1-1.8.1. Limma versions 1.5.0 and higher depend on R 1.9.0

limma limma

updated 22.1 years ago • Gordon Smyth

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 try: res…

Clustering flowClust Clustering flowClust

updated 13.8 years ago • Anja Mirenska

are all susceptible, at the second timepoint two of the species have gained resistance, and at the third timepoint they behave the same as at timepoint two. The third species remains susceptible during all three timepoints

deseq2 edger timecourse

updated 8.8 years ago • anna_stavrinides

Dear all, I'm analyzing microarray data using wgcna. I have 36 paired samples from 18 persons.Each person has two samples, one before a 6 week endurance training program,and one after the training program. We're investigating...is significantly different before and after exercise using paired-t-test.  3. For each person, compute the gene expression ratio( ratio=value before ex…

wgcna paired samples exercise

updated 9.4 years ago • 2323982403

--Hi all, I am struggling with a statistical question related to RNA seq data. I have collected cells sets and then extract RNA data from 6 different persons. I have 2 conditions: treated and untreated. At the end i have 12 libraries: 6 treated and 6 untreated. My goal is to find genes differentially expressed between the conditions. After recieving back the sequencing data (2x50bp illumin…

deseq2

updated 5.5 years ago • laurent.manchon

div class="preformatted">Hi, one of my collaborators is trying to install RSJava on Windows, for use with RMAGEML. I am not myself knowledgeable on Windows... Has anyone

RMAGEML RMAGEML

updated 20.8 years ago • Wolfgang Huber

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Microarray Microarray

updated 21.1 years ago • Yanqin Yang

We're looking for an additional person to work in our bioinformatics core facility within the Francis Crick Institute (a biomedical discovery institute

job bioinformatics uk Job

updated 8.7 years ago • Gavin Kelly

div class="preformatted">I'm trying to combine some of the microarray CEL files from the GEO series GSE7792 into an AffyBatch object using command 'read.affy' from package 'simpleaffy'. This command worked for other...files with different platforms (such as hgu133plus2, hgu133a and hgu95av2). For CEL files from this series, the annotation of the genes is from the 'huex10stv1' chip (Annotation:…

Microarray Annotation hgu133a hgu133plus2 cdf Microarray Annotation hgu133a hgu133plus2

updated 12.1 years ago • Rahmatallah, Yasir

it on a small amount of slides. I would like to do my study on a > larger scale now, with data (series of experiments) from other researchers > as well. My questions is the following: if I want to study, let's say 200 > slides...R at once (so together I mean, > with > read.affy() in package affy), or is it OK to read them series by series > (so > a…

hgu133a gcrma hgu133a gcrma

updated 21.6 years ago • Simon Lin

2): Vasa+/vasa- and the dye-swap (no SF at all) second(3 and 4): vasa-/vasa- SF and the dye-swap third(5 and 6): vasa-/vasa+ SF and the dye-swap fourth(7 and 8): vasa- SF/vasa+ SF and the dye-swap can I integrate this into one model matrix

updated 18.4 years ago • Aurelie Laugraud

like: design = ~ CellLine + Media + Vector + Media:Vector + CellLine:Vector + CellLine:Media The third being the LRT method design = ~ CellLine + Media + Vector + Media:Vector reduced = ~ CellLine + Media + Vector Any tips or advice would

deseq2

updated 7.0 years ago • jbard

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updated 7.3 years ago • dezer

variation from whole genome sequencing data. We have access to rich genomic data through close collaborations with clinical investigators at the institute. For further information visit our website <a href="http...Within this tri-institutional research and education community, postdocs can cultivate rewarding collaborations and participate in a rich agenda of academic, professio…

cancer genomics R computational biology bioconductor bioinformatics scientist Job

updated 9.3 years ago • weinhold

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updated 8.5 years ago • huisun.leong

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software engineer Job

updated 9.6 years ago • DanaFarber.Careers

This award is aimed to recognize outstanding long-term contributions to the project, for individuals who have provided excellent contributions in any form to the project over a substantial time period

Recognition Awards Bioc2022 Bioconductor

updated 3.7 years ago • shepherl

This award is aimed to recognize outstanding long-term contributions to the project, for individuals who have provided excellent contributions in any form to the project over a substantial time period

Bioconductor Bioc2021 Recognition Awards

updated 4.6 years ago • shepherl

This PhD project provides an exciting opportunity to develop methodologies for the analysis and comparison of high-throughput...More information and application at http://www.hbigs.uni-heidelberg.de/     project no. Boutros0115

high-throughput screening RNAi image analysis data integration visualization Job

updated 10.8 years ago • e.schmidt

This award is aimed to recognize outstanding long-term contributions to the project, for individuals who have provided excellent contributions in any form to the project over a substantial time period

bioc2020 bioconductor lifetime recognition awards News

updated 5.6 years ago • shepherl

BioC2026 will bring together researchers, developers, and community members to share knowledge, collaborate, and explore the latest in Bioconductor and bioinformatics. The website is now live at https://bioc2026.bioconductor.org

Bioconductor

updated 11 weeks ago • shepherl

<div class="preformatted">I am hoping someone can review my model and see if I am using the block argument in lmFit to correctly achieve a paired test. I have 12 samples made up of 4 people, each person is sampled 0hr, 4hr, and 22hr after exposure. The 12 slides are affy. I want to do a paired analysis using lmFit. My data looks like this: slide h0 h4 h22 person 1 1 0 0 1…

affy affy

updated 20.9 years ago • Dick Beyer

executed in your R session once you've loaded easyRNASeq. What analyses do you plan? I would personally not use RPKM for anything else than visualization. Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational...easyRNASeq package? > > > -- > Thanks & Regards, > > Amit Kumar …

Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq

updated 12.9 years ago • delhomme@embl.de

I'm trying to pull TCGA data as following: require(TCGAbiolinks) projects <- TCGAbiolinks:::getGDCprojects()$project_id projects <- projects[grepl('^TCGA',projects,perl=T)] query <- GDCquery...project = projects, data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", …

TCGAbiolinks TCGA

updated 5.3 years ago • aush

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...6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ************…

Normalization Preprocessing probe Normalization Preprocessing probe

updated 15.0 years ago • Manca Marco PATH

developing new tools, saving the natural world, or letting your curiosity run wild, we've got a project for you! **1. Method development:** Use novel autoML techniques to enhance gene network inference in single cell datasets...and ecologists. We welcome individuals with non-traditional career paths. Look for the projects supervised by 'Ezer'. Projects 1 and 3 can be signed up for here vi…

JobPosting

updated 13 months ago • Daphne

command: <pre> # All DNA methylation data for TCGA-COAD and TCGA-READ query.meth <- GDCquery(project = c("TCGA-COAD","TCGA-READ"), legacy = TRUE, data.category = "DNA methylation", platform = c("HumanMethylation450", "HumanMethylation27...flatten = flatten, ...) 4.fromJSON(url, simplifyDataFrame = TRUE) 3.getPr…

tcgabiolinks

updated 8.9 years ago • gaiusjaugustus