Bioconductor Forum

Documents/DMRcate$ git svn rebase Unable to determine upstream SVN information from working tree history</pre> Updating svn doesn't seem to help either: <pre> timpet@clark-lab:~/Documents/DMRcate$ svn --version svn, version 1.8.8...of contributions made by many people; see the NOTICE file for more information. Subversion is open source software, see http://subversion.apache.org…

git-svn bridge svn

updated 10.2 years ago • Tim Peters

I just found out that in recent reactome.db version (1.59.0) there was a change of pathways IDs (PATHID column). Before there was 20800 pathways with...Now there are 2185 pathways, shared between organisms. I'm not sure what were the reasons for the change, but I don't have problems with both schemes. However, I find it inconsistent, that for a single pathway ID there are multiple

reactome.db fgsea

updated 8.7 years ago • assaron

Ac27d.txt" "6-Cy5-Ac17d.txt" "27day" "17day" so after ... RG <- read.maimages(files, source="imagene") MA <- normalizeWithinArrays(RG) design=c(1,-1,1,-1,1,-1) fit <- lmFit(MA, design) . what direct are the fold changes I get

updated 17.5 years ago • Glyn Bradley

preformatted">Dear all, The new Ensembl marts for release 75 are live on www.ensembl.org. You can change your host to access our most recent data: mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path...Renamed Saccharomyces cerevisiae assembly from EF4 to R64-1-1 Added new Transcript source filter and attribute for all the species Added new filte…

Saccharomyces cerevisiae Vega Saccharomyces cerevisiae Vega

updated 11.9 years ago • Thomas Maurel

DEXSeq (only 2 biological replicates per condition), but other users should bare in mind that some changes in results might happen. Regarding my experimental design, I am building the DEXSeqDataSet object with only 2 conditions...on comparison for DEXSeq 1.10, sessionInfo is at the bottom of the email) On a matter of packages changes, and I put this question to discussion on the list, where sho…

Sequencing DESeq DEXSeq Sequencing DESeq DEXSeq

updated 11.4 years ago • António Miguel de Jesus Domingues

on [www.ensembl.org](http://www.ensembl.org/index.html). If you are using biomaRt, you can change your host to access our most recent data (With R 2.2 and Bioconductor version 3.1) ensembl\_mart\_80 <- useEnsembl...Updated rat (Rnor\_6.0) and zebrafish (GRCz10) assemblies * New Phenotype source filter in the "Phenotype" filter section * Renamed "APP…

biomart Ensembl zebrafish Rat 1000 genomes phase 3 News

updated 10.6 years ago • Thomas Maurel

related to detoxification (cytochromes, GST, etc..) are enriched in our dataset. We are using "Categories" and the "hyperg" function to do it. Do you suggest other type of analysis within "Categories" considering this objective

enrichment hypergeometric Categories

updated 4.6 years ago • josmantorres

for analyzing Agilent microarray data. I would like to know if it is possible to have access to the source codes of these packages so that I can better understand what is goind on in the background when we call each functions...Also, is it possible to edit the source code and run the package? Thanks a lot in advance, Regards, -- Karthik [[alternative HTML version deleted]] </div

limma AgiMicroRna limma AgiMicroRna

updated 13.6 years ago • Karthik K N

Only two spots remain for this course. Please contact me directly if interested but not yet registered. A two-day course on Bioconductor will be offered in Boston, April 4-5. Tuition $450 academic, $750 commercial. All proceeds...basics- april-4-5-2013 Space is limited. Questions to stvjc at channing.harvard.edu, or post comments on the blog site noted above. </div

updated 12.8 years ago • Vincent J. Carey, Jr.

it's not the first time that I use it). Something it's not right. It looks that some/many GO categories are missing... Here is some information: <pre> > x <- geneAnswersBuilder(subsetCL5_Genes, 'org.Hs.eg.db', categoryType...in geneAnswersConceptNet(x, color = "LogFC", geneLayer = 5, output = "interactive", : specified categories can not be recognized!</pre> I g…

geneanswers

updated 9.1 years ago • emiliomastriani

chip) library(limma) targets<-readTargets("targets.txt") RG<-read.maimages(targets$FileName,source="genepix",wt.fun=wtflags(0)) RG$printer<-getLayout(RG$genes) RG$genes<-readGAL("Y_pestis.sorted.gal") spottypes&lt...fit) tt<-topTable(fit,adjust="fdr",n=6000) write.table(tt,file="tmp.txt",sep="\t") I have also recently read about the Kooperberg method for b…

limma Category limma Category

updated 20.7 years ago • lepalmer@notes.cc.sunysb.edu

span style="line-height:1.6">s reactome gene sets come under subcategory of CP:REACTOME in category C2 of Broadset. can anybody correct given expression to make it executable ?</span> <span style="line-height:1.6">gtBroad...x, y, category="c2", </span><strong style="line-height:1.6">??_subset="cp:reactome"??_</strong><span style="line-height:…

globaltest

updated 9.8 years ago • Aditya Saxena

Recently, I am working on annotating the peak files using ChIPseeker. I am wondering is there away to understand the original...Recently, I am working on annotating the peak files using ChIPseeker. I am wondering is there away to understand the original genome distribution of each categories (promoter, 1st exon,  other exon, 1st intron, other intron, distal intergenic, etc.) from a speci…

chipseeker

updated 7.4 years ago • bright602

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080122/ 737fab2c/attachment.pl

updated 18.0 years ago • Yuan Jian

successful. Now, however, the install macOS system dependencies fails. This has been reported recently, e.g., https://github.com/actions/virtual-environments/issues/1864 and https://github.com/actions/virtual-environments

biocthis

updated 5.0 years ago • jeroen.gilis

if there is a way to subset the results from the analyzeVariants() function by different categories of splicing events, such as retained introns, Alternative first exons, Alternative last exons

sgseq

updated 8.6 years ago • amanda.joy.price

The 14 lineages fell out into 3 categories: high, average, and low. From there I selected two lineages from the high and two lineages from the low categories...non-exposed (control). What I am now trying to do is examine differential gene expression across the categories (high vs. low), across treatments (control vs. exposed), and the interaction between category and treatment. I've provided...a …

limma rna-seq edger random effects

updated 6.1 years ago • mjgarcia

about the locations of probes relative to 3' end and suppose the distances from 3' fall in 2 categories (X,Y). I am searching for a code that will enable me to partiotion probe-effect on the basis of the distance categories...X,Y). I want to have ANOVA table of the form, say Sources of variation DF SS MSS F Array 20 A Probe …

probe probe

updated 22.3 years ago • Stephen Nyangoma

div class="preformatted">Dear Chao-Jen, I recently noticed that the iFlow package was back up on the devel branch of Bioconductor, but I got an error message when I tried...to install it: > source("http://www.bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror...that it can be put back to the development branch (2.8) as soon as possibl…

iFlow iFlow

updated 14.9 years ago • Gabriel Nathan Kaufman, Mr

div class="preformatted">Hello I have had to review recently an analysis I did some time ago. This was done on affymetrix hgu133plus2 chips with R 2.4 and BioC 1.9 I have re-run...analyses using R 2.9 and BioC 2.4 (sessionInfo below). I have been surprised by the changes in the annotations: Many probesets that had had an annotation have become NA's whereas some have changed their symbol...1] …

Annotation hgu133plus2 Biobase annotate Annotation hgu133plus2 Biobase annotate

updated 16.5 years ago • Alex Sanchez

function. When I run GenTable, however, the results are strange. For example, for the GO:0006970 category, the geneID2GO mappings I used only lists 48 genes annotated to this category, but the GenTable function claims that...for it anywhere. Does anyone know why/how topGO is locating more genes than I give per GO category and from where they are getting pulled from? If my GO annotations are n…

GO Category topGO GO Category topGO

updated 12.4 years ago • Diana Toups Dugas

E-GEOD-21340.sdrf.txt",header=TRUE,stringsAsF actors=FALSE,sep="\t") # Looking to compare Family-history negativer versus Diabetis controls <- SDRF[grep("Control, Family History Neg",SDRF$Comment..Sample_source_name.),] disease

limma limma

updated 13.8 years ago • David Westergaard

legend of rowAnnotation() is the right side of the heatmap. However, I would like to put it in the left side of the heatmap. Is that possible? Also, how can I decrease the width of the annotation? I tried using the argument width

ComplexHeatmap

updated 5.5 years ago • AR3513

some issues on the analysis pipeline for the Epic version 2. Specifically, we wanted to know the source from where the CpG MAF is derived from, and where we can find the corresponding MAF for other ancestries (for example...we want to filter out >0.5 MAF for EUR, EAS, and AFR ancestries)? We are sourcing the v2 annotation here but could not find where the cpg_maf are sourced from: …

MethylationArray methy EPICv2manifest

updated 13 months ago • Meghan

<div class="preformatted">Hi, I'm having trouble getting GEOquery to work recently. On Ubuntu 9.10/R-2.10.1/BioC 2.6.1, GEOquery 2.11.3, download.file stops with "cannot open URL", On Ubuntu 8.04.1/R-2.9.2...div class="preformatted">Hi, I'm having trouble getting GEOquery to work recently. On Ubuntu 9.10/R-2.10.1/BioC 2.6.1, GEOquery 2.11.3, download.file stops with "cannot open URL"…

GEOquery GEOquery

updated 15.9 years ago • Gad Abraham

I have a relatively simple experiment, from which I have **Bulk RNASeq** samples from *two time-points* ("before" & "after") and *two treatments* ("drug" or "vehicle"). Recently, I tried to employ pathway analysis using BioConductor's **GSVA** package, mainly using the '*gsva*' and '*zscore*' methods. Several...samples from *two time-points* ("before" & "after") and *two treatmen…

GSVA RNASeq limma

updated 2.5 years ago • Jonathan

div class="preformatted">Dear all, I have recently started using R to draw heatmaps and have worked with several heatmaps in different packages(stats,gplots,heatplus...I am after, except for one thing. I would like to move the location of the color key from the top left to the bottom of the heatmap, and also alter its size to the length of the heatmap. Whilst I am able to alter various labe…

Heatplus Heatplus

updated 17.8 years ago • s.khalid@qmul.ac.uk

mailing list, I do a fair amount of work with the Affymetrix Zebrafish platform, but the recent move to .db annotation files seems to have left zebrafish behind. From what I've read in previous posts to the Bioconductor

Annotation zebrafish Annotation zebrafish

updated 17.3 years ago • Bio Sam

links that previously went to a download for the .tar.gz file (under the 'contributed' link on the left now go to a package description page just like the normal BioC packages. -J </div

GO GO

updated 23.4 years ago • Jeff Gentry

I have recently tried to implement the Samon-Tximport-DESeq2 pipeline with my latest RNA-Seq dataset however I have a problem with...cohort and I am looking at more covariates of interest than disease status (age, gender, family history etc etc). Many thanks, Matthew

deseq2 wgcna salmon rna-seq DESeq2

updated 7.7 years ago • mad6kj

how those fitted values might be obtained when the TMM-normalized cpms do not reveal that behavior (left-hand plots). In the latter case, cpms tend to 0 except for one repeat on the WT strain. I thank you in advance for any help/comment

RNA-Seq edger fitted values differential expression normalization

updated 6.6 years ago • David Rengel

Hi all, I want to analyze the databases of 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...havent mentioned which kind of database they are using for analysis. Can any one provide a better source from where i can download This open source databases for analysis. &…

ppi bioinformatics

updated 10.4 years ago • beingseema03

the hypergeometirx test from GOstat for mutliple testing, since one performs many tests (over all GO categories found in the gene list). I'm not sure if correction for multiple testing makse sense since the GO terms are highly...does not perform any kind of multiple testing correction, is this right? I'd be happy to receive comments on this and to heare about your experience. kind regar…

GO GOstats GO GOstats

updated 21.4 years ago • Arne.Muller@aventis.com

Recently, I reanalyzed some gene expression data using DESeq2. To my surprise, the resulting volcano plots looked quite different...RStudio), and the VST normalized counts for both Galaxy and RStudio files. 1) Would you please comment which fold change will be closer to reality? 2) Why am I getting such a discrepancy in the log2FoldChange between the

DESeq2

updated 2.6 years ago • peTTU

step and checked in the check step. 2. Running check in this way will not have any side-effects (left behind files) in your package source directory. It is, of course, a bit tedious to build and check. So while you are working...on code, you may find it convenient to occasionally run check on the package source directory. Hope that helps clarify things. + seth </div

updated 20.3 years ago • Seth Falcon

RNA expression signature of two patient groups. Initial analyses with LIMMA indicate that there is a source of variation which contributes more to the variance within the sample groups than between them. In a PCA the samples...while a covariate (or covariates) contribute(s) to PC1. So far we have not been able to identify the source of variation in PC1. What can I do to model the unknown covaria…

limma covariate

updated 6.8 years ago • scheran02

<div class="preformatted">>> Message: 7 Date: Fri, 01 Aug 2008 15:52:22 -0400 From: "Deanne >> Taylor" <dtaylor at="" hsph.harvard.edu=""> Subject: [BioC] Is anyone >> developing an extensible Galaxy-like interface for Bioconductor? To: >> <bioconductor at="" stat.math.ethz.ch=""> Message-ID: >> <…

Genetics Annotation Genetics Annotation

updated 17.4 years ago • Ross Lazarus

of our Lab, Prof. Curtis Huttenhower. The package was developed originally by Emma Schwager who has left our Lab. I cloned the package, made the necessary changes, ran a successful BUILD and CHECK, committed the changes and am...ready to push the changes,  but I am getting a "permission denied" message - and indeed, I see in my profile I can update only ccrepe. I need update

software error

updated 7.2 years ago • george.weingart

Is there a way to change the font size of the annotation axis values? These values often overlap, is the sizing automatic (circled in red below...Example (not my code): [code source][2] set.seed(123) mat = matrix(rnorm(100), 10) rownames(mat) = paste0("R", 1:10) colnames(mat) = paste0("C", 1:10) column_ha = HeatmapAnnotation

ComplexHeatmap

updated 3.5 years ago • nalaspina

I am just wondering, if there are people fitting LOESS on a subset of unchanged genes and any comment on that. Thanks in advance! Yiwen From: Davis, Sean (NCI) Sent: Wednesday, May 13, 2009 9:01 AM To: He, Yiwen (NIH/CIT) [C] Cc: bioconductor...at stat.math.ethz.ch Subject: Re: [BioC] Normalization of arrays where most of the genes change On Wed, May 13, 2009 at 8:54 AM, He, Yiwen (NIH/CIT) […

Normalization vsn limma Normalization vsn limma

updated 16.7 years ago • Alicia Oshlack

403 Forbidden 13:53:40 ERROR 403: Forbidden. ) If I go to /repository/release1.5/package/Source/ and click hexbin_1.0.10.tar.gz I get the message: Forbidden You don't have permission to access /repository/release1.5...package/Source/hexbin_1.0.10.tar.gz on this server. The link to the source package does not seem to go to any package. Is there in fact...a source package somewhere? From what …

GO hexbin arrayQuality GO hexbin arrayQuality

updated 21.2 years ago • Darlene Goldstein

4.7 Image-derived Spot Quality Weights", there are examples of setting weights to genepix and spot sources provided. According to my zero experience, I do have no idea how to do this properly with files of 'agilent' source. Would

updated 12.3 years ago • Guest User

to make a fork of the repo to try a fix. Is there a way to specify to install the package from source from our repo? Thanks

install package fork bugfix

updated 3.8 years ago • Jeff

Hi everyone, We apologize for the recent spam attack. There were hundreds of posts within a very short time, making the site unusable. It was especially painful...Hi everyone, We apologize for the recent spam attack. There were hundreds of posts within a very short time, making the site unusable. It was especially painful for those users who received every post via email.  The site was…

security spam News

updated 9.7 years ago • Dan Tenenbaum

the ballgown output for differential expression analysis. I see only positive values in the fold changes. From the earlier posts, I found that FC<1 indicates down regulation and FC>1 indicates upregulation. In my...case, I used 2-group comparisons where the labels were control and inoculated and in another category, it was resistant vs moderately resistant. So I am not sur…

changes ballgown

updated 7.3 years ago • amy16

my gene is on the - strand, which means that the order of the exons in the expression plot is from left to right, but the order of the exons in the gene model is from right to left  (according to the strand). How is this fixable

rnaseq r dexseq visualization

updated 8.7 years ago • aleipz

that it doesn't make a huge difference (and almost none in practical terms), but I'm curious. I've left the parameter absMu1 at 1 (as I understand it, this represents effect size, as fold change of at least 2). My sigmaD parameter...R. [R.app GUI 1.52 (6188) x86_64-apple-darwin9.8.0] [Workspace restored from /Users/jms/.RData] [History restored from /Users/jms/.Rapp.history] > library(…

qPCR GUI qPCR GUI

updated 13.3 years ago • Michael Salbaum

sampleNames in an exprSet object. I would like to get rid of the .CEL portion of the file name (or change it altogether) that occurs when I use ReadAffy() and rma() to create an exprSet. To put it into context, I am calculating additional...lt;- pd > newexprSet <- new('exprSet',exprs=exprs(origexprSet),phenoData=pd) In the most recent version of R/BioC, this produced an error (E…

affy affyio affy affyio

updated 19.4 years ago • Jeff Lande

potential two outlier samples see the plot here ![MDS plot][1] For me the red dot on the far left and one red on the far right down could be outliers ! Any comment on this issue [1]: /media/images/23532710-cdaf-4a70-a9d2-6e7cf025

edgeR

updated 3.7 years ago • Mohamed

preformatted">Dear BioC list and Biocore Data Team, we are using various Agilent arrays and the recent paper by Gertz et al. ( http://www.biomedcentral.com/1471-2164/10/566 ) made me feel a little bit uneasy about the annotation

Annotation hgug4112a oligo Annotation hgug4112a oligo

updated 15.9 years ago • Axel Klenk

sending again now that I'm a member of the list) There appears to be a broken link in the "Sources Of Data" section of the Bioconductor web page. The "Unigene Annotation For Affy Chips" link doesn't work. The most obvious

Annotation affy Annotation affy

updated 23.6 years ago • Colin A. Smith

div class="preformatted">Dear All, we're trying to get the source code for logit-t. Despite several inquiries to the authors, we haven't had any luck so far. Can any of you help out? Thanks

updated 21.6 years ago • Detlef Weigel

https://waldronlab.io/curatedMetagenomicData/articles/available-studies.html) do not include all the recent curated studies as listed in https://github.com/waldronlab/curatedMetagenomicDataCuration/tree/master/inst/curated...per https://waldronlab.io/curatedMetagenomicData/index.html. Therefore, I did not see those most recent curated studies. Could you advise how could I access the most recent d…

curatedMetagenomicData

updated 2.9 years ago • yingliu3

bound peaks with __View__ in R, wondering how you sort by the index rather than one of the categories such as fold change? Thanks. Rob &nbsp

R diffbind

updated 8.8 years ago • rbronste

<div class="preformatted">Dear All, I'm have data txt files from Agilent's 60mer Arabidopsis slides that were created using Agilent's feature extraction software, and am trying to read them into limma (using Bioconductor) and have encountered the following problem. I can read in my targets file just fine but with the follow up command: "RG <- read.maimages(files=targets$FileName, …

Genetics limma Genetics limma

updated 21.2 years ago • André Chanderbali

style="line-height: 1.6;">www.ensembl.org</a><span style="line-height:1.6">.</span> You can change your host to access our most recent data: * ensembl\_mart <- useMart(biomart="ENSEMBL\_MART\_ENSEMBL", host="[www.ensembl.org...section</span> * <span style="line-height:1.6">Renamed "Reference ID" to "Variation Name" and "Source description" to "Variati…

ensembl biomart Vervet-AGM News

updated 11.3 years ago • Thomas Maurel

Dear all, can anyone provide me an older source of biocFileCache (ideally 1.2.0)? This is due to the fact that our institution HPC cluster runs with R 3.3.3. The oldest

biomaRt

updated 3.1 years ago • julian.konzok

is this: 1) Nonspecific filtering to remove ~50-70% of genes that are 'absent' (Affy chips), don't change much, etc.. 2) Use rank products to get two-tailed p-values for remaining genes. Rank products (papers in FEBS letters and...for 'Breitling r[au]' and you'll find 'em) 3) Use ks.test() to compare genes from each ontology category to the rest of the genes that are not represented in that on…

Genetics GO GOstats Category topGO Genetics GO GOstats Category topGO

updated 18.5 years ago • Ken Termiso

div class="preformatted">I checked source code for summarizeOverlaps method in Rsamtools package and found that it calls some internal function .processBamFiles...processBamFile") no object named '.processBamFile' was found In the end, I downloaded the Rsamtools source package and located the source code chunk for function .processBamFiles. But this is kind of awkward. Anyone knows why...and …

Rsamtools Rsamtools

updated 12.5 years ago • heyi xiao

programming API that we provide. In theory, it should shield developers from the hassles of format changes. And when you're developing to one or a few operating systems and/or distributing binaries to your customers, then...And Affymetrix can't promise that formats will remain stable, but we'll publish what those changes are -- warts and all -- for those that want them. We prefer that BioCondu…

Microarray GO Network Cancer cdf affy PROMISE Microarray GO Network Cancer cdf affy

updated 22.5 years ago • Kulp, David