Bioconductor Forum

Tenure-track Group Leader Position in Computational Biology =========================================================== The Department of Experimental and Health Sciences ([DCEXS][1]) of the Universitat Pompeu Fabra (UPF) aims to fill a Tenure-Track Group Leader position in Computational Biology, who will also serve as Scientific Lead of our Computing Core Facility ([SIT][2]). We encourage ap…

bioinformatics sequencing barcelona proteomics

updated 4.8 years ago • Robert Castelo

in running a GWAS for a binary phenotype in a diverse ancestry dataset using GENESIS. In the bioRxiv paper (https://doi.org/10.1101/409953) I had read that GENESIS was using the LMM OPS model. In the latest paper of Gogarten et al

genesis

updated 5.4 years ago • o.giannakopoulou

Hi, I'm confused about the nature of the data used in the ALL example in Bioconductor. The paper (Chiaretti et al 2004) describes a study of T-cell ALL and doesn't mention BCR-ABL, while the Bioconductor example (e.g. in...the Genome Biology paper) works through a comparison of BCR/ABL v. ALL1/AF4, which are, I think, markers for B-ALL. I can't find anything in the phenoData

updated 18.1 years ago • Thomas Elliott

Hi there, I am trying to implement the kTSP algorithm defined in the switchBox package, in matlab but am having some trouble seeing the appropriate source code in R. What source files are used for this algorithm? Right now I have implemented the scoring of the gene pairs (all possible combinations) but can't seem to figure out what to do to break ties. In the papers written about this algorithm,…

kTSP switchBox MATLAB TSP

updated 10.4 years ago • katherine.beaulieu14

2021-01-15 [1] CRAN (R 4.0.0) #> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.0) #> GenomeInfoDb * 1.26.2 2020-12-08 [1] Bioconductor #> GenomeInfoDbData...highr 0.8 2019-03-20 [1] CRAN (R 4.0.0) #> htmltools 0.5.1 2021-01-12 [1] CRAN (R 4.0.0) #> IRanges * 2.24.1 2020-12-12 [1] …

DropletUtils emptyDrops 10x

updated 4.9 years ago • Peter Hickey

to find differently expressed genes, and to maximise the use of available data...as there are many papers I have read that conducted experiments on U133A&U133B chips (on the same sample set), however in their result/discussion...sections the papers seems to show only one figure In this particular paper that I am trying to understand how they found differently expressed

updated 13.2 years ago • Zack Will

there a way to search the most significant genes associated to a specific disease mentioned in some papers? Because for e.g. the top 5 genes are not mentioned in any paper to be related to some diseases. The table is formed by 40000

GeneExpression RNASeqR limma

updated 5.0 years ago • Will

div class="preformatted"> Dear all, I came across a paper mentionning package called MedlineR. However the original link mentionned in the paper (http://dbsr.duke.edu/pub/MedlineR

updated 17.2 years ago • David Enot

Hi, I'm trying to install KEGGprofile to do analysis in R but it says it's not available for BioConductor 3.13 yet. But the website says it is. sessionInfo results might be a little weird since I installed a bunch of other BioConductor packages today. ``` BiocManager::install("KEGGprofile") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details …

KEGG RNASeq

updated 4.5 years ago • Sophie

gt; BiocManager::install("GenomeInfoDb") Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) Installing package(s) 'GenomeInfoDb' trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib...are in the temp file as indicated above. ```r sessionInfo( ) R version 4.1.1 (2021-08-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 1…

zip GenomeInfoDb

updated 4.3 years ago • David

div class="preformatted">*CALL FOR PAPERS* * * *and* * * *CALL FOR POSTERS* * * *1st International Conference* *on* * * *Bioinformatics Research and Development* * B I R D '07*** *http://www.birdconf.org...of Science, Israel Erik Sonnhammer, Karolinska Institute, Sweden and about 200 other PC-members * * *Paper Submission Details: *Authors are invited to submit original research…

Pathways microRNA Pathways microRNA

updated 19.4 years ago • Prof.Roland Wagner

div class="preformatted">*CALL FOR PAPERS* * * *1st International Conference* *on* * * *Bioinformatics Research and Development* * B I R D ?07*** *http://www.birdconf.org <http...of Science, Israel Erik Sonnhammer, Karolinska Institute, Sweden and about 200 other PC-members * * *Paper Submission Details: *Authors are invited to submit original research contributions or experience…

Pathways microRNA Pathways microRNA

updated 19.5 years ago • Prof.Roland Wagner

<div class="preformatted">Dear all, Im sorry if this is a question not directly related to using bioconductor packages, but at least I used them for the analysis that I need a reference to ;o) I have a biopsy related project with 63 unpaired biopsies in total and two groups where I cannot find any differences using limma, probably due to tissue heterogeneity. I wonder if there is anyone w…

limma limma

updated 17.4 years ago • Johan Lindberg

viewform) to nominate someone or self nominate. The deadline for nominations is May 31, 2021

Bioc2021 Awards Recognition Bioconductor

updated 4.6 years ago • shepherl

Dear Friends, I have been having considerable difficulty doing various package related bioconductor actions. Here is my system specifications: ======================================================================= macOS Monterey Version: 12.3 (21E230) MacBook Pro (Retina, 13-inch, Early 2015) Memory: 16 GB 1867 MHz DDR3 RStudio 2021.09.0 Build 351 R version 4.1.2 (2021-11-01)…

packages installation Bioconductor updating

updated 3.7 years ago • jose

to understand how exactly the gcrma software works, and working my way through the Wu/Irizarry paper "A Model Based Background Adjustment for Oligonucleotide Expression Arrays" . My problem is in understanding the Bayes...like. Could anyone point me towards a source of the functions or a source with more detail than the paper I mentioned above? Any help would be very much appreciated, Best regar…

gcrma gcrma

updated 19.3 years ago • Anne Pohrt

The expected number of attendees (estimating minimum and maximum values); * Description of paper review process and acceptance standards; * A draft workshop call for papers; * The expected date and duration of the workshop...workshop; * Advertising the workshop and issuing a call for participation/papers; * Collecting and evaluating submissions using the BIRD conference …

PROcess PROcess

updated 18.1 years ago • Prof. Roland Wagner

2009 Los Angeles/Anaheim, USA http://world-research-institutes.org/conferences/CSIE/2009 CALL FOR PAPERS & EXPO The Los Angeles/Anaheim area is known for its many renowned attractions, such as Disneyland, Universal Studios...Symposium CSIE 2009 conference proceedings will be published by the IEEE Computer Society and all papers in the proceedings will be included in EI Compendex, ISTP…

updated 17.3 years ago • Hongping Wu

CRAN: https://cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Warning message: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'org.Hs.eg.db

org.Hs.eg.db org.H

updated 4.0 years ago • 2041792073

https://forms.gle/d9PyAjAw62yVKxjL8) to nominate someone. The deadline for nominations is May 31, 2021

Bioconductor Bioc2021 Recognition Awards

updated 4.6 years ago • shepherl

Hi, In the Nat Prot paper about Ballgown, it's said as follow: _Note that Ballgown’s statistical test is a standard linear model-based comparison...And second, how should the step(regularization) be taken during the ballgown procedure as this paper? I am a noob and hurried, who can help me and provide a detailed command? Thank very much

limma rna-seq

updated 8.1 years ago • zoukai3412085

<div class="preformatted">I have been having an on-going discussion with a colleague about whether he can say that some genes are "absent" in some tissues based on two-color microarrays - most recently, Agilent arrays. There are a number of reasons that he would like to do this which are a mix of biology and QC. He wants to use some (arbitrary) normalized expression level, or unnormalized…

Sequencing Sequencing

updated 16.9 years ago • Naomi Altman

__Johnson and Li. 2007, Adjusting batch effects in microarray expression data using empirical Bayes methods__, is the paper for the comBat package, and I have trouble understanding the following from page 119  ..... stabilize gene variances by __shrinking variances across all other genes__, possibly protecting their inference from artifacts in the data. In this paper, we extend the EB m…

ComBat microarray batch effects

updated 8.4 years ago • DataFanatic

I have my data as __.mat file__ (from Matlab), and I want to process it with '__MassSpecWavelet__' package to find its peaks. I tested this code, <pre> > path <- system.file("mat-files", package="R.matlab") > pathname <- file.path("d:", "Prony Paper") > data <- readMat(pathname)</pre> and I get this reply from R; <pre> Error in f…

process

updated 11.2 years ago • s.kazemi.n

div class="preformatted">Hello, I just read a paper that I actually strongly recommend: "Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined...control dataset" PMID 15693945 In this paper they advice to do 2 normalization steps, one after the background correction and one on the expression summary (using

Normalization Normalization

updated 20.4 years ago • Emmanuel Levy

<div class="preformatted">Hi, I'm trying out the alternative splicing commands from the paper, M.J. Okoniewski and C.J. Miller "Comprehensive Analysis of Affymetrix Exon Arrays using BioConductor". (2008) PLoS 4(2): 1...div class="preformatted">Hi, I'm trying out the alternative splicing commands from the paper, M.J. Okoniewski and C.J. Miller "Comprehensive Analysis of Affymetrix Exo…

updated 17.0 years ago • dorothyc

install.packages("BiocManager") Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) > > BiocManager::install("xcms") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories...CRAN: https://cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Old packages: 'class', 'for…

xcms Install

updated 3.8 years ago • Fanny-shufan

CRAN: https://cran.rstudio.com/ Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.1.1/library packages: survival

limma edgeR Biobase GeneExpression

updated 4.3 years ago • sogol.bouyeh

form of financial underwriting. **Applications closed: 5pm Tuesday (Eastern Australian time) 11 May 2021

australia cancer wehi

updated 4.3 years ago • Gordon Smyth

<div class="preformatted">I'm using the timecourse library to calculate Hotelling's T2 statistics, and would like to convert these to P values (and, ultimately, perform FDR). For a 4 time point, 3 replicates (control and treated each), 54K gene experiment, I'm struggling with the appropriate variables for transformation. This paper: http://bioinformatics.oxfordjournals.org/cgi/content/…

TimeCourse convert timecourse TimeCourse convert timecourse

updated 19.6 years ago • aaron.j.mackey@gsk.com

<pre> Hello, I am trying to use DEXSeq for the first time and I am encountering this error. I am closely following this paper: "Inferring differential exon usage in RNA-Seq data with the DEXSeq package " I am using my own data. The files correspond to: </pre> <pre> countFiles = 37 samples with counts generated as suggested in the paper.</pre> flatte…

dexseq

updated 8.6 years ago • cpsosa0006

Protein Protein Interaction which are open source and freely available. I have gone through the paper which is " An evaluation of human protein-protein interaction data in the public domain" by Suresh Mathivanan, Balamurugan...BIND, DIP , MIPS , PDZBase , and Reactome. The links of the available databases are mentioned in the paper but there is a list of databases available in it. They have…

ppi bioinformatics

updated 10.3 years ago • beingseema03

Hi, I am trying to build a weighted network using WGCNA. While reading their paper (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559#Sec1), I found they have used TOM for...Hi, I am trying to build a weighted network using WGCNA. While reading their paper (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559#Sec1), I found they have used T…

WGCNA TOM

updated 5.7 years ago • n.naharfancy

The expected number of attendees (estimating minimum and maximum values); . Description of paper review process and acceptance standards; . A draft workshop call for papers; . The expected date and duration of the workshop...system . Together with the organizers, determining the workshop date and time; . Publication of the papers in the proceedings of BIRD'08. Workshop organizers will be respons…

PROcess PROcess

updated 18.4 years ago • Prof. Roland Wagner

to PGSEA package and GSEA method and hope to get some replies: 1. After reading the following paper, I think the theoretical basis for PGSEA is very different from GSEA (Broad, MIT). So, my first question is, is there a package...downloaded from GSEA website before, though). http://www.biomedcentral.com/1471-2105/6/144 2. The paper above mentioned comparison of two "groups" of samples for a s…

PGSEA PGSEA

updated 17.3 years ago • Weiwei Shi

<div class="preformatted">Dear users, I would like to draw your attention on a recent paper by Lim et al (Bioinformatics, 2007): "Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks" Bioinformatics 2007 23(13):i282-i288; doi:10.1093/bioinformatics/btm201 http://bioinformatics.oxfordjournals.org/cgi/content/full/23/13/i282 This paper r…

gcrma gcrma

updated 18.2 years ago • Pierre Neuvial

sva.html This version includes support for both surrogate variable analysis, as described in the papers: http://www.biostat.jhsph.edu/~jleek/papers/sva.pdf http://www.biostat.jhsph.edu/~jleek/papers/framework.pdf and...Combat, an approach for removing batch effects when the source of batch is known as described in the paper: http://biostatistics.oxfordjournals.org/content/early/2006/04/21/bio…

Regression limma sva Regression limma sva

updated 14.0 years ago • Jeff Leek

I see more and more papers these days that use a read cut off before deseq2 analysis, I wonder what is the rational and/or how do they arrive at how...many reads is a right number..for example from one of the papers ```DESeq2 was applied to genes having more than 20 reads in half the number of samples``` ^ this study had n=8 4wt and 4ko. i could

deseq2 rnaseq

updated 6.4 years ago • badribio

nbsp;which is used for computational deconvolution of microarray expression datasets. Their [paper](https://www.ncbi.nlm.nih.gov/pubmed/25620908) demonstrates its usage on human brain microarray data. The paper

deconvolution rnaseq psea

updated 7.9 years ago • WouterDeCoster

The expected number of attendees (estimating minimum and maximum values); * Description of paper review process and acceptance standards; * A draft workshop call for papers; * The expected date and duration of the workshop...Together with the organizers, determining the workshop date and time; * Publication of the papers in the proceedings of BIRD'08. Workshop organizers wi…

PROcess PROcess

updated 18.0 years ago • Prof. Roland Wagner

not provided by package 'gdsfmt' > sessionInfo( ) R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.6 LTS Thank you for your help

SeqArray gdsfmt

updated 3.8 years ago • Hanan

forms.gle/d9PyAjAw62yVKxjL8) to nominate someone or yourself. The deadline for nominations is May 31, 2021

awards bioc2021 recognition community Bioconductor

updated 4.6 years ago • shepherl

<div class="preformatted">Hello everybody, I am a french student in bioinformatic. I have to analyze microarray data and I have some questions about prefiltering genes. The dataset that I have to analyze consist in 8 microarray, i have 4 times points and 2 replicats for each time point. Agilent's two color microarray (Whole Mouse Genome (4x44K) Oligo Microarrays) were used for the analysi…

Microarray limma oligo Microarray limma oligo

updated 14.5 years ago • Stephanie PIERSON

Firefox (92.0) but will display on Safari (14.1.2). For my most recent attempt, I updated R to 4.1.1 (2021-08-10) on my macbook (macOS Big Sur 11.5.2) and re-installed msaR and it is still not displaying on Chrome and Firefox. I happen...browser. Has anyone else had this issue? Thanks! LA ```r sessionInfo( ) R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Runni…

Chrome msaR Firefox browsers

updated 4.3 years ago • amon

you for the wonderful pipeline. Apologies in advance, I have tried to find this answer in your code/paper, but still dont understand. When I get a a summaryDT from summary(fit, doLRT = condition) -- I was looking at the correlation...and contrasts), but the logFC z-scores are ~0.2 with the hurdle p-values. If I understand from the paper you are summing the Wald/LRT test statistics to derive …

MAST

updated 15 months ago • Greg

In the paper of Love (2014) it says about the initial GLM: > To get a gene-wise dis- persion estimate for a gene i, we start by fitting a negative...initial fitted values \hat{\mu}_ij^0? I would be very glad to get an explanation for this or a paper/book to read this in

GLM prior DESeq LFC

updated 3.5 years ago • stew

cel file name (Wangyaping normal and disease condition, organism HOMO Sapiens). I have used this paper (Microarray Data Analysis for Transcriptome Profiling) command line RUN in Rstudio, Some result has come out such as...line has to RUN the result come out Error in ncol(eset) 'eset.filt' not found. I have atteched this paper PDF. Please sort out this problem. Thanks Dear ![enter image descript…

oligo package

updated 6.7 years ago • cpyadav22

been working on variance stabilization techniques for cDNA microarrays. I have been studying the papers: I. Rocke and Durbin, (2001), `A model for measurement error for gene expression arrays', J. Comput. Biol, 8, 557--569 and II. Durbin...for most of the genes I replicate (and for my data). I wonder if someone is aware of other related papers to that subject (not only by those authors). Is the…

Microarray Microarray

updated 20.6 years ago • E Motakis, Mathematics

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080219/ 964432ef/attachment.pl

updated 17.8 years ago • Eleni Christodoulou

easy to use! However, I couldn't find it explicitly stated anywhere in the vignette, the original paper, the SCAN help page nor searching on the support site what scale the resulting normalized values are on. From their distribution...for my samples is only from -1.8 to 5.2, I assume it's not the standard log2? The equations in the paper use log() in several places, so it's on the natural log sca…

scan.upc

updated 10.4 years ago • Jenny Drnevich

<div class="preformatted">Hi, I am outputting various plots to pdfs, including heatmaps and the like. What I would like is for the plot to fill the whole of the A4 sheet of paper rather than just a square in the centre. This would increase the readability of a large heatmap no end. Has anyone got any ideas how to achieve this? I am currently using pdf("filename", paper="A4"). Thanks …

Cancer a4 Cancer a4

updated 18.8 years ago • Daniel Brewer

div class="preformatted">I'm reading through some papers that use PAM to create a classifier from microarray data. I would like to use these classifiers to classify my own samples...with microarray data. These papers publish the output of 'pamr.listgenes()', and it's not clear how to massage that into a format that 'pamr.predict()' will accept

Microarray Microarray

updated 12.6 years ago • Ed Siefker

I'm a happy user of the DNABarcodes package by Tilo Buschmann. I came across the paper by Hawkins, John A., Stephen K. Jones, Ilya J. Finkelstein, and William H. Press. 2018. “Indel-Correcting DNA Barcodes for High...resulting in wrong > barcode decodings (SI Appendix) ... Buschmann & Bystrykh 2013 is the paper on which the DNABarcode package is based. I coudn't quite follow th…

single-cell sequencing barcodes

updated 6.6 years ago • Philip Lijnzaad

coverage between conditions etc.) will be applied to these windows, if ws =100. I've seen a paper (PMC4213696) apart from MEDIPS's original paper that researchers are using ws = 100 only.  My question is what is the

medips medip-seq peak finding luckas

updated 8.6 years ago • anupriyaverma1408

Hello, I am trying to install package destiny on R_4.1.0 via Bioamanager 3.13, however, It warned me that no package destiny available. ```r > BiocManager::install('destiny') 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.13 (BiocManager 1.30.1…

destiny BiocVersion

updated 4.5 years ago • Yiming

well as use some of the more advanced analysis tools on them. Can anyone point me to any published papers or working papers on slide design that cover these points: * single/duplicate/triplicate/many spots * advantages of replicate...gene's, lighthouse spots, blanks, buffer spots etc) - this is a huge topic and there are a few papers out there on this, but if someone wants to comment ... Search…

Microarray affy Microarray affy

updated 22.5 years ago • William Kenworthy

I ran R in windows 10. In the paper("_Multiple Co-inertia Analysis of Multiple OMICS Data using omicade4_"), they use  the NCI60\_4arrays to analyse...I ran R in windows 10. In the paper("_Multiple Co-inertia Analysis of Multiple OMICS Data using omicade4_"), they use  the NCI60\_4arrays to analyse, and...https://photos.google.com/photo/AF1QipO_NvYbhGF0XwBM8yJcbBYUtLTgUdlpOmpU…

omicade4 R plotVar

updated 8.7 years ago • weiiioyo

for these unsupervised analyses to avoid potential bias? thanks in advance! ``` R version 4.1.2 (2021-11-01) limma_3.50.3

limma limma-voom

updated 12 months ago • Ahdee

Ontology http://current.geneontology.org/ontology/gobasic.obo With a date stamp from the source of: 2021-09-01" (per GO.db manual)? *Or* is there a possibility that the GO.db package will reference an updated version of the GO ontology

GO.db versioning

updated 3.9 years ago • rebeliscu

Hello, I have submitted the package rmspc to Bioconductor in July 2021. A prerequisite for the rmspc package is .NET 5.0. Before installing the rmspc package, the program .NET 5.0. should already

build BuildReport

updated 3.9 years ago • Meriem