Bioconductor Forum

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 11.2 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

I am using goseq for category testing of differentially expressed genes in my RNA-seq data sets and I wanted to extend it to categories other than...the GO categories. Specifically, I wanted to make use of the molecular signatures database (MSigDB). To be clear, I am not trying to do...a ranking approach like GSEA. I would simply like to take advantage of the extensive list of categories in MSigD…

goseq category test

updated 7.3 years ago • Mthabisi Moyo

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 7.2 years ago • bdy8

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

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

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

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

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

There is a build error showed up with both release and devel version of pathview package since several days ago. And multiple users also complaint on a emerging parsing error (the same issue as the build error) as below:   > library(pathview) > data(gse16873.d) > pv.out <- pathview(gene.data = gse16873.d\[, 1\], pathway.id = "04110", +  …

pathview KEGGgraph gage pathway pathway analysis

updated 8.4 years ago • Luo Weijun

Treatment 2) has been generated. A fold-change is then used to enrich the data set for genes that show within class activity (i.e. select only genes that show a mean...fold change between classes). This filtered data set is then used for differential testing. My first question is: How is this different...wise sample space reduction should be subject to the same criticism? Secondly, the supervi…

Pathways Pathways

updated 17.5 years ago • Johan van Heerden

peakAnnoList, title = "MeA F/M Peak Annotation")</pre> In the current form plotting 11 annotation categories and want to be able to cut down on what the plot displays, by eliminating some (e.g. 5' UTR) and combining some (e.g. peaks...at varying distances from promoter into one promoter category). Was attempting to use to cut down on the categories: <pre> genomicAnnotationPriority&…

chipseeker chipseq annotation

updated 8.1 years ago • rbronste

randomForest) use test sample set and train sample set to do prediction. To create the expreSet, the category is needed for each sample. However sometimes we need to predict sample without its category. Anybody has some clue

Category Category

updated 21.4 years ago • Liu, Xin

after some initial analysis I have a list of genes (2000 or so). I want to now classify them into GO categories. I know there are lots of web based tools to do this but I want to do this in R. Has anyone done this before ? (I am sure, someone

GO Arabidopsis thaliana GO Arabidopsis thaliana

updated 16.5 years ago • Vishal Thapar

<div class="preformatted">Hi, I have been trying to generate GO category table for Chinese hamster genome using getgo function in goseq package. Even though chinese hamster is said to be...div class="preformatted">Hi, I have been trying to generate GO category table for Chinese hamster genome using getgo function in goseq package. Even though chinese hamster is said to...included in th…

GO Category goseq

updated 11.3 years ago • upendra kumar devisetty

what is Software, Annotationdata, Experimentdata and workflow category?Explain

Software annotation experiment workflow

updated 5.4 years ago • gnanaprakash.s

<div class="preformatted">Dear all, We have performed a time-scale experiment including different time- points (0h, 2h, 6h, .). Treated and untreated cells were compared by competitive hybridizations on every time-point using dual-channel microarrays. Now we want to detect groups of genes affected by the same TFs using a gene clustering approach based on the set of differentially expresse…

Clustering Cancer Clustering Cancer

updated 18.4 years ago • Serge Eifes

div class="preformatted">Beyond the scope of the manual and vigenettes of Category and GOStats, I would like to understand more about ChrMapHyperGParams and linearMTest. After successfully using

Annotation GOstats Category Annotation GOstats Category

updated 16.7 years ago • Daren Tan

preformatted">Dear members, I am seeking for an efficient way to sort the genes into different categories. I am working on the analysis of the microarray data and now I encounter a problem. After getting the differentially...expressed genes, I want to sort them into different categories according to their functions. However, I find it hard to set up a criteria to classify them. Now I am tryi…

Microarray GO Microarray GO

updated 18.9 years ago • De-Jian ZHAO

<div class="preformatted">Dear biomaRt users, Tomorrow the Ensembl BioMart database will fix it's current Ensembl 47 release with the following attribute/filter name changes involving gene symbols. * For the hsapiens_gene_ensembl (human) dataset you'll need hgnc_symbol as attribute and filter...BioMart database will fix it's current Ensembl 47 release with the following attribute/filter n…

biomaRt biomaRt

updated 18.1 years ago • Steffen

Dear all, I am new to the field. I have recently worked with two datasets and noticed that in both cases (in my hands) data transformation appears to change the sample

DESeq2 rld vsd data transformation ntd

updated 6.1 years ago • Arctic

As far as I understand, using limma's "removeBatchEffect" enables to remove only two batches categories by defining "batch" and "batch2" removeBatchEffect(x, batch=NULL, batch2=NULL, covariates=NULL, design=matrix(1,ncol

limma

updated 5.9 years ago • Matan G.

Hi all, I have a good amount of experience in doing differential gene expression analysis in two categories like healthy samples and disease patients. Now I have three categories of patients at baseline, then at week 16

anova

updated 8.5 years ago • pbachali

double counted. I am following pipeline for RNA-seq analysis and would like to know any suggestions/comments regarding the pipeline: 1. Mapping the reads using Tophat 2. Convert Tophat output.bam to Sam 3. Create bed file from

convert DESeq convert DESeq

updated 13.9 years ago • Akula, Nirmala NIH/NIMH [C]

stat.math.ethz.ch Subject: RE: [BioC] KNN, SVM,and randomForest - How to predict samples without category By definition, in supervised learning you always train (with known catagories), then run your unbiased data through...stat.math.ethz.ch Subject: [BioC] KNN, SVM,and randomForest - How to predict samples without category Dear all, Supervised clusterings (KNN, SVM, and randomForest) use test…

Category Category

updated 21.4 years ago • Liu, Xin

reasons, the matchGenes function in bumphunter was hardwired to use the hg19 TxDb. This has changed in the latest devel version (1.7.3) to be general. It is available right now from github `` (devtools::install_github...with the right column names (chr, start, end) None of this has been tested thoroughly so comments and bug reports are welcomed

annotation bumphunter News

updated 11.1 years ago • rafa

tool would you recommend in order to display a heatmap of the genes clustered based on a shared GO category (eg "chromatin") ?  thank you,    bogdan   &nbsp

goexpress gopro

updated 8.8 years ago • Bogdan

that issue. So, I prefer using DESeq2 normalization. But I cannot use DESeq2 for getting log2 fold change values because I don't have replicates for some of the experimental conditions and DESeq2 needs replicates to estimate...log2 fold change values. So, I want to manually calculate log2 fold change values from DESeq2 normalized counts. So, I am using log2(DESeq2norm_exp...0.5)-log2(DESeq2norm_c…

DESeq2 DifferentialExpression

updated 3.0 years ago • Jayesh Kumar

I wondered if anyone could comment on what is generally considered the most appropriate method of calculating fold change values from Affy...I wondered if anyone could comment on what is generally considered the most appropriate method of calculating fold change values from Affy data. I have a data set from a test vs. control experiment (n=3 i…

affy limma gcrma siggenes

updated 8.8 years ago • Peter White

Hello, I have noticed a strange behaviour when using Rsubread in a recent bacterial RNASeq dataset. The use of the nTrim parameters lead to a change in the order of the reads provoking that they

Rsubread

updated 2.1 years ago • glopez

I'd a question regarding a recent change in the Rsubread package. I routinely deal with mixed paired end and single end data. The Rsubread function featureCounts

software error Rsubread

updated 5.5 years ago • barrel0luck

is updated to the latest version. I used to used this function in R 2.4.X and the low version of category , and it works. But when I used the updated version, it goes wrong. Any advise? Yun [[alternative HTML version deleted]] </div

Annotation probe Category Annotation probe Category

updated 16.2 years ago • LIYUN

<div class="preformatted">Hi, all, The developmental version of annotation packages (1.6.0) is now available and can be accessed by doing (using hgu95av2 as an example): > library(reposTools) > install.packages2("hgu95av2", develOK = TRUE) The following changes/additions have been made: a. Environments pkgNameNM and pkgNameNP (e. g. hgu95av2NM) no longer exist…

Annotation GO Organism hgu95av2 mguatlas5k mgug4121a rgug4130a probe Category Annotation

updated 21.6 years ago • John Zhang

through the goseq vignette and adapting it to my own dataset. ?I have got my list of enriched go categories, which looks like this: > head(GO.wall) ? ? ? ? category over_represented_pvalue under_represented_pvalue 3217 GO...but this just gives me a list of ALL the genes attached to this GO category. ?I?would like to find out which of my DE genes are in this GO category. I have…

GO Category goseq GO Category goseq

updated 9.7 years ago • Helen Wright

<div class="preformatted">Dear allI have been working recently on drawing GO graphs of the significantly changing GOs, and have extensively used the instructions for the packages GOstats and TopGO for drawing the post-analysis results (hyperGTest or Fisher's test, respectively) for drawing the GO graphs. I am trying to do this for some yeast data that we collected in a previous project. Unf…

GO Yeast GOstats topGO GO Yeast GOstats topGO

updated 17.3 years ago • balag Ganesan

it loads properly. I get the following error output, however, when I try to run hyperGTest, package Category, on a vector of Entrez Gene IDs and a vector of the gene universe of the chip. I suspect I did something wrong when building...0.05, conditional = TRUE, testDirection = "over") > params A GOHyperGParams instance category: GO annotation: ragene10stv1 > hyperGTest(params) Err…

Annotation Category AnnotationDbi Annotation Category AnnotationDbi

updated 17.2 years ago • Mark W Kimpel

However, I was wondering if there is a way to display/list the genes belongig to each GO enriched categories. Thanks in advance. [[alternative HTML version deleted]] </div

GO

updated 11.3 years ago • artur

such as KNN, SVM, and randomForest. However, all the train and test put into them require KNOWN categories. The code evaluates the accuracy by comparing the PREDICT categories of the test (created by supervised clustering...with their KNOWN categories. So I wonder to know how to predict the test WITHOUT KNOWN categories. Xin -----Original Message----- From: Sean Davis [mailto...Subject: Re: [Bi…

Microarray Category Microarray Category

updated 21.4 years ago • Liu, Xin

annotation distributed with bioconductor of hgu133plus2 is from 2005. Does anyone have built a more recent annotation ? There is a lot of new information around that is not included in the annotation package. I am trying with

Annotation hgu133plus2 AnnBuilder Annotation hgu133plus2 AnnBuilder

updated 19.0 years ago • Marco Zucchelli

<div class="preformatted">I am using Limma for an experimental design with three categories, two biological replicates each and two technical replicates of each biological replicate for a total of 12 arrays...div class="preformatted">I am using Limma for an experimental design with three categories, two biological replicates each and two technical replicates of each biological replicate …

limma limma

updated 12.5 years ago • James Platt

Hi All, I am trying to make my own package a little easier to use, and want to extend some of the Category parameter classes. I can easily extend the primary virtual class without any problems, but I run into difficulties...there is no package called '.db' This behavior seems to be caused by the DatPkgFactory function in Category, but I can't figure out how to get around it in the class definit…

Annotation GO Category Annotation GO Category

updated 15.0 years ago • Robert M. Flight

A research article at BMC Bioinformatics: BACKGROUND: When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names. RESULTS: A little detective work...arounds and scripts for circumventing the problem. URL: http://www.biomedcentral.com/1471-2105/5/80 -- Comments? Post your replies to http://bioinformatics.org/forums/forum.p…

Microarray Microarray

updated 21.4 years ago • David Lapointe

currently working on a differential gene expression analysis and I've used GOSeq to find enriched GO categories, just like what is mentioned here (https://stat.ethz.ch/pipermail/bioconductor/attachments/20110308/92b2 7df4...tairgo <- read.table("ATH_GO_GOSLIM.txt", header=F, sep="\t", fill=T) #read in GO Categories File GO.wall <- goseq(pwf, gene2cat=tairgo[,c(1,6)]) # get ID and G…

GO Organism PROcess goseq GO Organism PROcess goseq

updated 11.8 years ago • Dale Richardson

div class="preformatted">I have recently started to use bioconduct to analyze a time course study with U133A and B, which has 7 time points including time...needed from Bioconductor user group. I used the following step to filter the significant changing genes: filter by call flag; by control signal (GeneSpring feature, no effect on rma and gcrma data set); t-test and ANOVA...46 (Li-Wong PMonl…

Normalization Clustering affy gcrma GeneSpring Normalization Clustering affy gcrma

updated 21.8 years ago • Lizhe Xu

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

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

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

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 9.0 years ago • emiliomastriani

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

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 4.9 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 8.5 years ago • amanda.joy.price

Hello, My current project is examining variation in cold tolerance and cold-induced changes in gene expression across isogenic fly lines. The basics of the project is that I phenotyped 14 isogenic lineages...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…

limma rna-seq edger random effects

updated 6.1 years ago • mjgarcia