Bioconductor Forum

The Pathview Web server](https://pathview.uncc.edu/) was recently published in Nucleic Acids Research (NAR) Web Server issue: https://academic.oup.com/nar/article-lookup/doi/10.1093...database synchronization   -open access to all analyses and resources   -analysis history and data sharing via free registered user accounts   -complete online help and documen…

pathway analysis visualization data integration omics pathview News

updated 8.7 years ago • Luo Weijun

Hello everyone. I recently started using GOSEQ for the analysis of RNA-Seq results from DESeq2. I have around 37K total genes with ~3K differentialy...command. It works fine, however gives me a warning : <pre> For 16675 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation

goseq mm9

updated 10.7 years ago • Vivek.b

div class="preformatted">Figure 5 in the recent Nucleic Acids Research 2003, Vol. 31, No. 4 e15 (http://nar.oupjournals.org/cgi/content/full/31/4/e15/GNG015F5) shows an interesting...asymmetry in the distribution of fold changes for non- spiked in genes. Can anyone comment on the reason for this? Here, dChip has the least amount of bias. Thanks, Chris

updated 22.4 years ago • Chris Paulse

div class="preformatted">Thanks to all who have sent comments and suggestions. I would like to ask one more question. I am doing the filtering to prepare a dataset for some several...coming from 7 known biological classes, but comparing the means of these groups to look at fold change would bias the method. Assuming intersample normalization is it justified to compare the overall highest with …

Normalization Normalization

updated 21.5 years ago • peter robinson

class="preformatted">dear group, is it possible to get list of genes contributing to enrichment of a category in GoStats. for example: apoptosis is enriched as a GO category. now I want to get list of genes responsible for that...category. is it possible in gostats. thanks Ad. </div

GO GOstats Category GO GOstats Category

updated 16.7 years ago • Adrian Johnson

Hello all, Here is a very simple question that I couldn't figure out after hours: How can I change the appearance of the in ggplot? The closest I could get to the basic R graphics is by using opts(axis.line = theme_segment...Still very unpleasant! Thanks for you comments' Robert </div

updated 13.8 years ago • Faryabi, Robert NIH/NCI [F]

I noticed that MAST sometimes has NA for the continuous coefficient. When this happens, it also has NA for the estimated fold change. I couldn't find much in the documentation about this, but I was wondering if someone can explain it? This is a problem for...has NA for the continuous coefficient. When this happens, it also has NA for the estimated fold change. I couldn't find much in the documen…

scrnaseq MAST differential gene expression

updated 8.4 years ago • Andrew_McDavid

new Ensembl marts for release 102 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ``` ensemblmart102 <- useEnsembl(biomart=“ensembl") ``` On behalf of Ensembl Team. As...commented on the previous release 101 message (thanks to @Mike-Smith), if you want force one previous version you can use: ``` ensembl_101

Ensembl biomaRt BioMar ensembldb

updated 5.1 years ago • mchakiachvili

span style="line-height:1.6">Can anyone help with a (proper) way of testing for MSigDB categories enrichment using hypergeometric test?</span> I am looking something along the lines like we do testing for GO/KEGG...PFAM categories first by creating an instance of HyperGParams subclass (e.g. GOHyperGParams or KEGGHyperGParams) and then calling

category gostats msigdb hypergeometric test

updated 10.4 years ago • petyuk

boost (www.boost.org) C++ headers for graph algorithms are now derived from boost 1.49 2) RBGL C++ sources have been modified to compile cleanly with g++ 4.7 This has necessitated (at least temporary) removal of boost-based...functions. The loss seems unimportant given the availability of Rgraphviz There has been a minor change to the behavior of incremental.components Similar changes are i…

graph RBGL graph RBGL

updated 13.6 years ago • Vincent J. Carey, Jr.

Download the installation script getBioC.R. 2. Start the R program typing "R" at the shell prompt. 3. Change the working directory to be the directory where you saved the file getBioC.R, e.g., "setwd("~/Project1")". 4. Type the command...source("getBioC.R")" at the R prompt to source the installation script into your R session. Alternately, you could paste the entire...of the script into your R …

updated 22.7 years ago • Henrik Bengtsson

<div class="preformatted">Can someone help? Thanks a lot in advance. ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan@fhcrc.org> Date: Thu, Dec 24, 2009 at 5:35 PM Subject: Re: [R] Question to use R plot GO pie chart To: "Waverley @ Palo Alto" <waverley.paloalto at="" gmail.com=""> Cc: r-help at r-project.org Waverley @ Palo Alto wrote: > Hi, &…

GO Cancer Category GO Cancer Category

updated 16.0 years ago • Waverley @ Palo Alto

  Hi there, I am having problem with the DEXseq package. I want to test if the exon usage of honey bee (Apis mellifera) has changed after infection. As the DEXseq package suggests, I downloaded the honey bee genome fasta file and the annotation gff...problem with the DEXseq package. I want to test if the exon usage of honey bee (Apis mellifera) has changed after infection. As the D…

dexseq reads

updated 8.6 years ago • 514028929

saved and a "warm start" (http://www.coin-or.org/SYMPHONY/man-5.1/node129.html) could be used after changing some of the parameters (or after acquiring a new supply of patience). Instead of being left with "nothing" and having...to start all over again... Any comments would be very welcome! Chiel Bakkeren &nbsp

lpsymphony R parameters control warm start

updated 9.6 years ago • chiel

from the Trinotate pipeline), I ran GOseq and found a good number (67) of over-represented GO categories, but I had zero under-represented categories, which makes me think something went awry in my R script. My general...question is this: is it reasonable to expect to have a large number of over-represented categories and few to no under-represented categories?  Admittedly, I am new to …

goseq go enrichment

updated 7.5 years ago • mart1139

subjects and I'd like to estimate the Survival function. Does the Icens package take into account left truncation and if so how? Thanks

Icens Survival Left-truncation Interval-Censored

updated 6.4 years ago • fabiana.gordon

expression. Broadly, groups are age/sex matched but have added noise due to complex medical histories, which are matched as best as possible but is still far from perfect. Ran through a basic analysis limma pipeline...to different population demographics for study #2), which will be published separately. What I am left with is the ability to create secondary, also age/sex matched control group…

limma multtest

updated 12 months ago • Ali Barry

hi list, I recently upgraded my R to 3.1.2 and DESeq2 to 1.6.3.  I re-run some of my code on a RNAseq experiment.  Comparing to the...old results (done in R 3.1.0 and DESeq2 v1.4.5), all the estimates (e.g. fold changes, p values) have changed.  It seems that the most dramatic changes happened to those genes with large fold changes...genes are those with low read count…

deseq2

updated 10.9 years ago • Shi, Tao

will be out of the office starting Wed 02/01/2006 and will not return until Sat 02/07/2060. I have left the SGDP. I am contactable at matthewwilkesnash at hotmail.com. </div

updated 19.5 years ago • M.Nash@iop.kcl.ac.uk

and workflow packages will be maintained as git repositories created to capture the full commit history of each package. (the commit history of the 'data\_store' portion of data experiment packages will unfortunately not...The build system and other core infrastructure will use git.bioconductor.org as the canonical source after the transition.   * Developers may wish to indepen…

git svn infrastructure bioconductor News

updated 8.5 years ago • nitesh.turaga

vpList(vpStack(viewport(x=0.1, y=0.1, w=0.5, h=0.5, just=c("left", "bottom"), name="B"), viewport(x=0.1, y=0.1, w=0.5, h=0.5, just=c("left", "bottom"), name="C"), viewport(x=0.1, y=0.1, w=0.5, h=0.5, just=c("left", "bottom…

Gviz Gviz

updated 11.9 years ago • Dan Du

I am wondering if the reference category in a covariable will affect the result of assocTestSingle? Any suggestions are appreciated

assocTestSingle GENESIS

updated 2.9 years ago • SuperD

Hello, We recently deployed a version of the support forum, in these changes include a migration to reset handles. They have to be explicitly

Bioconductor handles

updated 4.8 years ago • natay.aberra

div class="preformatted">Dear Bioconductor, I have installed the Category package 1.0.1 on my Windows 2000 computer, after installation of R 2.1.0 and other packages required by Category...survival 2.17; splines -- no longer listed in Bioconductor package list) I would like to use the Category package for microarray data analysis. I am not an experienced R user, so I get easily confused. Th…

Microarray hgu95av2 Category Microarray hgu95av2 Category

updated 20.6 years ago • Neefs, Jean-Marc [PRDBE]

We have decide to delay the release 3 days to allow the build report to stabilize from some recent changes/issues that have since been remedied (connectivity issues, missing system dependencies, etc...) The **release of...schedule](http://bioconductor.org/developers/release-schedule/) has been updated to reflect these changes. **NOTE:** R has released R-3.6.0  officially this morn…

release deadlines News

updated 6.7 years ago • shepherl

div class="preformatted">Hi everyone, Is there a way to retrieve the level for a GO category in R? As of now I am retrieving terms by using the following code: > BP_terms <- stack(lapply(mget(GO_BP_Cats_5_more_genes...category, GOTERM, ifnotfound=NA), Term)) Now I wanted go get the level (3,4,5...,9). I looked into the "annotate" package and the " .db" (I am using

GO Category GO Category

updated 14.1 years ago • Biase, Fernando

What is the procedure to obtain source code for the functions within the STRINGdb package? ```r string_db <- STRINGdb$new( version="11", species=9606, score_threshold...I would like to understand the process behind the function `string_db$map()` and tweak it to change the functionality of the method. I couldn't find the code in the Package Archive here: https://bioconductor.org/packag…

STRINGdb Bioconductor

updated 4.9 years ago • deepue

zooms in) and negative expands (zooms out)." _ Then there is the code example with a confusing comment (IMO). <pre> > ir * -2 # half the width</pre> because this is doubling the width of the original ir

iranges

updated 10.9 years ago • Michael Love

Hello All, I am looking for a way to adjust the height of the left labels. I have edited the bottom and can move expand the quartz window to make them more visible but this is impossible

r R heatmap

updated 7.0 years ago • coyoung

then I looked at More information on results columns which says  log2 fold change (MLE): condition treated vs untreated" but it does not explian anything more . This is the explanation given here For a...gene, a log2 fold change of -1 for `` condition treated vs untreated `` means that the treatment induces a multiplicative change in observed...unt…

deseq2

updated 7.8 years ago • Bioinformatics

into cancer. in my class file CL0 = normal and CL1 = Cancer I wrote a function to compute fold changes. I would like some help from group members to comment on this function to calculate fold changes. 1. is there a better...way to calculate. 2. how do i get log-fold changes. fc <- function(x,CL0,CL1){ x0 <- x[,CL0] x1 <- x[,CL1] res <- (apply…

Cancer Cancer

updated 19.7 years ago • Srinivas Iyyer

div class="preformatted">Hi All, I am developing a package that depends on Category. As part of my package development, I decided that I should use R CMD check and documentation examples to verify that...Run using "R --vanilla" to be similar to R CMD check, but still fails in a normal R session as well source(file.path(R.home("share"), "R", "examples-header.R")) options(warn = 1) options(page…

Category Category

updated 14.9 years ago • Robert M. Flight

Esteemed BioC user's, I'm struggling to achieve some details of a heatmap using heatmap.2(): 1. Change label locations, for both rows & columns from the default right & bottom, to left and top. Can this be done within heatmap.2...this default behavior (how) and call a new function to relabel (what) specifying locations? 2. Change the angle of the labels. By default column label…

updated 15.5 years ago • k. brand

div class="preformatted">Hi, How do you recommend to clean up the Illumina gene titles for Category analysis? Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La

Category Category

updated 17.3 years ago • Lana Schaffer

Kind of a basic question, but I am trying to install the following TF footprinting package and running into a problem: https://sourceforge.net/projects/bagfootr/?source=typ\_redirect R does not allow installation of bagfoot\_0.9.6.tar.gz because it has two dependencies that I...TF footprinting package and running into a problem: https://sourceforge.net/projects/bagfootr/?source=typ\_r…

package installation dependencies bagfootr bagfoot

updated 8.2 years ago • rbronste

in a state with a p-value of about 0.04, was now no longer significant with 0.06. Not all states changed, however. The input data is identical, the scripts are identical yet the old outcome is no longer reproducible. I am...Both run on Kubuntu 16.04 with R 3.3.1. The only difference is that on the computer with the changed results, I updated Bioconductor to 3.4 (from 3.2) and updated all package…

deseq2 new version bioconductor software error reproducibility

updated 9.2 years ago • Daniel Elsner

div class="preformatted">I am working my way through the Category vignette and have a question as to how the t statistics for categories are computed from the incidence matrix and...on the bottom of page 3 (development version vignette) and is as follows: There are 135 pathways (categories)... A = AmER2 %*% tobs$statistic A = tA/sqrt(rs2) ames(tA) = row.names(AmER2) I know this is matrix mul…

Pathways Category Pathways Category

updated 18.4 years ago • Kimpel, Mark W

You'll notice that interface to the support site has been updated. The interface is simpler and more consistent, with major changes that include: * User-specific information is in a blue bar at the top of the page, main action items are centered with the...to the support site has been updated. The interface is simpler and more consistent, with major changes that include: * User-specific inf…

news News

updated 11.3 years ago • Martin Morgan

<div class="preformatted">The deadline for the 2.10 Bioconductor release is very close. There are a few packages that depend on or suggest edgeR. This email is to alert developers to changes in edgeR that might potentially break code. One of the changes below was made only two weeks ago, so I thought it would be worth an email to alert people. 1. estimateCommonDisp() and estimateGLMComm…

edgeR edgeR

updated 13.8 years ago • Gordon Smyth

Hello, I am Enio Gjerga and I have recently obtained the role of the maintainer for the CNORfeeder and the CNORode package. I am facing trouble trying to access...the source packages for then later syncing it with a Github repository and do a few necessary updates. I try first to obtain developer

CNORfeeder CNORode

updated 5.8 years ago • enio.gjerga

Apparently the version of AnnotationDbi packages in the Bioconductor 3.9 release was bumped recently. It was 1.46.0 before, now it's at 1.46.1 (see https://bioconductor.org/packages/3.9/bioc/html/AnnotationDbi.html...Apparently the version of AnnotationDbi packages in the Bioconductor 3.9 release was bumped recently. It was 1.46.0 before, now it's at 1.46.1 (see https://bioconductor.org/pac…

download

updated 6.4 years ago • kenneth.hoste

7.983866 9.034676 9.043481 8.896545 10.052179 10.091817 ``` I estimated the log2 fold change (C vs A) based on the rlog values, that, the mean of rlog values in C minus that in A. The resulting fold change estimate will...change (that is, 15.24) in DESeq2 and compared that to the one (15.31) I calculated previously, and they were very close. After looking...at the manual and paper, I thoug…

DESeq2

updated 4.3 years ago • ting.chen.lrx

8) must equal sample number in assay data (0). I have a question for lumi developers, were there changes in the most recent version of the lumi package that would make such code stop working? I can send the entire script, but...I thought that maybe it isn't necessary (in the case when this is a known change in behavior). Here's the sessionInfo(): R version 2.9.2 (2009-08-24) i386-pc-mingw32 …

lumi lumi

updated 16.3 years ago • Michal Blazejczyk

am doing this, after extracting all the contrasts I am going to group genotypes by a arbitrary risk category made from experimental data (low, medium and high) and look at the response of all the low risk genotypes VS the high...risk genotypes to pull out risk specific gene changes for these. I then am going to see how these identified genes change between other risk categories. I understand I co…

deseq2 DeSeq2

updated 7.3 years ago • bdy8

<div class="preformatted">Hi: I recently tried generating the cel image form a cel file of type 133A. I am noticing that the GeneChip HGU 133 A mark appears on...div class="preformatted">Hi: I recently tried generating the cel image form a cel file of type 133A. I am noticing that the GeneChip HGU 133 A mark appears...the bottom left as opposed to the Top left of the image. Any ideas …

updated 22.9 years ago • Sundaram, Shyam NIH/CIT

div class="preformatted">Hello all, I want to alert you to some upcoming changes related to the Bioconductor website. We are in the process of moving the primary website from its current location...We have a semi-working prototype which can be viewed here: http://bioconductornew.mycontent.org/ Comments are welcomed, but please do not report broken links to us at this time --- we haven't yet …

PROcess PROcess

updated 21.0 years ago • Seth Falcon

Hello, I just noticed an odd behavior of bg.adjust.gcrma - I thought it was only supposed to change the pm values, not mm values, according to the help page: "The returned value is an 'AffyBatch' object, in which the PM probe...intensities have been background adjusted. The rest is left the same as the starting 'AffyBatch' object." However, my mm values are changing (example code below) f…

drosgenome1 cdf Biobase reposTools affy gcrma affyPLM simpleaffy affyQCReport affyio cdf

updated 19.6 years ago • Jenny Drnevich

is there any package in bioconductor that allows me to apply Fishers exact test on my own annoated categories. I would be using the entire genome or chip as the reference. Thank you. Ad. </div

updated 16.4 years ago • Adrian Johnson

<div class="preformatted">Hi, I would like to do a category analysis on our data set. I had learning vignettes on BioC Subview of Annotation and I found goProfiles package very...div class="preformatted">Hi, I would like to do a category analysis on our data set. I had learning vignettes on BioC Subview of Annotation and I found goProfiles package...me if there are some ways for to d…

Microarray Annotation GO Category Microarray Annotation GO Category

updated 17.5 years ago • Marcelo Laia

<div class="preformatted">When I try to use biocLite to upgrade my Rsamtools under R-devel, biocLite reports that it tries to use the 2.8 repository (correct), but it tries to download Rsamtools 1.1.17 whereas the version of Rsamtools installed using R-2.12 is version 1.2.0 (later than 1.1.17) and the version accessible from subversion is version 1.3.2. I suspect this has something to do w…

Rsamtools Rsamtools

updated 15.2 years ago • Kasper Daniel Hansen

Hi, I've been using Gviz and while I really like the package, one thing that annoys me is the automatic scaling of the width of the title panel to the left based on the size of the plot pane in RStudio. When making several different plots, I'd like to make sure the title panel is...package, one thing that annoys me is the automatic scaling of the width of the title panel to the left based on t…

Gviz

updated 4.6 years ago • rheery

developers and all, I'm testing RNA-Seq data with the following factors: treatmentA , with the categories 0,1 treatmentB ,  with the categories 0,1,2 batch , with the categories 0,1,2,3 the goal is to detect genes in which...MDS plot, different groups include different number of individuals, and different representation of categories. For example: in the batch\_0 group, treatmen…

edger

updated 9.3 years ago • assaf www

the code that creats the 'lmat' matrix that is used to ses the layout. Everything else can be left as it is now. -Greg Author of gplots::heatmap.2 On Mar 31, 2008, at 12:37PM , James W. MacDonald wrote: > Hi Khalid, > > s.khalid...at qmul.ac.uk wrote: >> Dear all, >> >> I have recently started using R to draw heatmaps and have work…

Microarray Cancer Heatplus Microarray Cancer Heatplus

updated 17.8 years ago • Gregory Warnes

div class="preformatted">Hi, Has biocLite.R changed recently? We are (recently) getting errors using this non-interactively via Rscript using R 2.15.3. Here's a minimal...example on a fresh 2.15.3 installation: $ Rscript -e "sessionInfo(); source('http://bioconductor.org/biocLite.R')" R version 2.15.3 (2013-03-01) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale...grDevices utils …

updated 11.7 years ago • David Eby

DE) expression analysis using RNA-seq data and I have used GOseq to find enriched Gene Ontology (GO) categories in the DE genes list. I have a couple of questions to ask, and hope someone can help me: Can I extract the number of genes...and IDs present in each enriched category using GOseq? If not, I suppose it is better to annotate all the genes for GO and find out which genes are annotated i…

GO annotate Category goseq GO annotate Category goseq

updated 14.8 years ago • Biase, Fernando

2009?11?4? 14:34 To: LIYUN Cc: bioconductor Subject: Re: [BioC] function error for "hyperGTest" in Category package Please keep the dialogue on the mailing list. The maintainers of the package may comment on this phenomenon...in the following sequence: > ########### > library( GO.db) > library(Category) > library(hgu133a.db) > libra…

Annotation GO hgu133a probe GOstats Category Annotation GO hgu133a probe GOstats

updated 16.2 years ago • LIYUN

citation information is not its corresponding paper but an R package citation. I am wondering how to change the citation in my R package source files. Many thanks for your great help! Xiangyu

citation

updated 7.4 years ago • xyluo1991

Hi everyone, I've recently started using DESeq2 version 1.20. Since there were several changes, I decided to start my pipeline from scratch

deseq2

updated 7.4 years ago • andrebolerbarros

take a while... Selecting significant annotations. Warning messages: 1: Ontology MF has no GO terms left. in: prepareGOannotation (parent at data@uniqueid, object at meta, object at ontologies, 2: Ontology BP has no GO terms left...parent at data@uniqueid, object at meta, object at ontologies, 3: Ontology CC has no GO terms left. in: prepareGOannotation (parent at data@uniqueid, object at meta, o…

Annotation GO Yeast mgug4122a goCluster Annotation GO Yeast mgug4122a goCluster

updated 20.0 years ago • Yong Jiang

I assume i will get considerably less fluctuated expressions across exons. To do that, I have changed the countData in before plotting, (i know the analyze is based on count data, therefore i did not do that at the beginning...gene/exon ENSG00000182718 failed, coefficients for this gene won't show up. NULL</pre> Should I change something from source code ? So, any comments and h…

dexseq plotdexseq

updated 8.1 years ago • tanerarslan.gen