Bioconductor Forum

<div class="preformatted">Greetings all, We've received a few bug fixes that have been merged into the BioC 1.6 release repository: gcrma 1.1.4 Resourcerer 1.1.2 Ruuid 1.5.3 Source packages and Windows binary packages are available on www.bioconductor.org. Mac OS X binary packages will be available next week. Details of changes: gcrma 1.1.4 Removed unnecessary variables in mem.bkg…

updated 20.6 years ago • Seth Falcon

combines the two scans into a single results file. It turns out that the results file format had changed because when our scanner was serviced the settings were changed. I realize now that I would have had to specify the...measurements and the column definition in the read.maimages function in limma (I'm using v2.16.4) source="agilent" is G = "gMeanSignal",Gb = "gBGMedianSignal", R = "rMeanSigna…

limma limma

updated 16.9 years ago • Coleman, Ilsa

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 8.5 years ago • Luo Weijun

I have not yet found a convincing argument for or against this practice. I would like to make a comment and would appreciate any constructive feedback, as I am not a Statistician but a Biologists. As far as I can see the...has been divided into 2 categories: (1) "Supervised" and (2) "Unsupervised" filtering, where (1) is based on some knowledge regarding the functional classes...wise sample spac…

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 21.5 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

nbsp; Basically what I would like to know to make my plot perfect, is wether it is possible to left align the titles of the single tracks including the GenomeAxisTrack and GeneRegiontrack.   Best, Alex &nbsp

gviz title text formatting grid

updated 7.1 years ago • alex.gos90

<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 16.8 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 19.0 years ago • De-Jian ZHAO

gene sets. for cDC2 i have a very high AUC score, but for some reason no cells are assigned to this category. If I understand the way the AUC scores are calculated, a high AUC means, many of the genes in the cDC2 gene-set are expressed...but in the middle plot (created with `AUCell_plotTSNE`) none of the cells are assigned to this category. From what I've read, the reason might be connect…

AUCell

updated 3 months ago • gogeni5529

The source code provided with the voom paper uses a function called `` qAbundanceDist ``, which gets loaded through the `` load `` statement...qAbundanceDist" > class(qAbundanceDist) [1] "function" </pre> If I try to view the source code for this function, what I get is this: <pre> > qAbundanceDist function (v) .approxfun(x, y, v, method, yle…

voom

updated 9.3 years ago • kjo

We are pleased to announce that the new Ensembl marts for release 85 are now live 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: ensembl\_mart\_85 <- useEnsembl(biomart=“ensembl")   * Ensembl Genes 85 * New "Gene-order conservation score" and "Whole-gen…

ensembl biomart release85 ensembl release mart News

updated 9.5 years ago • Thomas Maurel

<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 18.2 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.

<div class="preformatted">Hi Marc Thank you very much for your answer, and I'm really sorry for my much belated reply. I have tried your suggestion, but if I use KEGGFrame directly it gives me an error that the pfam ID's are not valid KEGG ID's (See below). I suspect that what you have in mind is not what I have attempted here, but instead to create my data object manually by specifying…

SNP Annotation GO Organism affy GOstats Category SNP Annotation GO Organism affy

updated 14.0 years ago • Henrik Hjarvard de Fine Licht

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]

Yes","No"))</pre> Looking at the results I get about thousands genes with absolute log fold change > 0.5. However, when I run the following command: <pre> resGA <- results(dds, lfcThreshold=0.5, altHypothesis="greaterAbs...pre> I only get 256 with absolute log fold change > 0.5. Anyone can help me figure out what is the source of this discrepancy? Thanks

lfcthreshold deseq2

updated 8.0 years ago • lirongrossmann

biolinux community www.biolinux.org , I put at your disposition R-BioC for R 2.5.x for fedora core 6. Comments for improvement will be welcome. It is not an official fedora rpm because fedora plans to support only R. Unfortunatly...fc6 rpm for now but they are more for previous fc It works well, and it contains 102 very usefull sources: abind adSplit affxparser affy affycomp affydata affyio affyl…

updated 18.1 years ago • D.Enrique ESCOBAR ESPINOZA

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 21.5 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

div class="preformatted">I've recently started using the option to put group labels below the features in Gviz 1.8.1 AnnotationTracks (just.group="below...algorithm does not move the features onto a separate line as it does when justification is to the left. See the example photos: just.group="left": http://imgur.com/VfUN3G0 just.group="below": http://imgur.com/zmRGtxD I have been...widths…

Gviz Gviz

updated 11.6 years ago • Lance Parsons

Dear All: 4 days are left to register for a week-long short course on quantitative mass spectrometry-based proteomics, May 18-22, 2015 at Northeastern

proteomics news course massspectrometry News

updated 10.8 years ago • Olga Vitek

<div class="preformatted">On Fri, Jul 25, 2014 at 2:32 PM, Kaj Chokeshaiusaha <kaj.chk@gmail.com> wrote: > Dear all, > Thank you very much for your comments. I now feel confident to stick > with the usual approach. > There is one thing that sticks in my mind all the time. This is > probably due to my lack of basic knowledge. I'm wondering about peop…

updated 11.5 years ago • Sean Davis

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

Dear Bioconductors, I've found the page http://bioconductor.org/data/metaData.html which has source packages for drosophila2cdf and drosophila2probe, but I can't find the source for drosophila2 itself. Is this supposed

drosophila2 cdf drosophila2 cdf

updated 20.8 years ago • Cyrus Harmon

will work as a temporary fix for this issue. In my case, I fixed the issue by: 1- Cloning the source repository from `Bioconductor` `git clone https://git.bioconductor.org/packages/Guitar` 2- Changing the following line...having to specify the source package when called (in any of the scripts located in `Guitar/R`): `GenomicRanges:reduce()`. 3- Load all the R scripts belonging...…

GenomicFeatures Guitar txdbmaker GenomicRanges

updated 8 days ago • ferran.llobet

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_control+0.5) for calculating log2 fold change values. I am not sure whether it is a good idea or the choice of pseudo-count here is very critical. The other option I guess...of the normalized counts. By doing this I believe I c…

DESeq2 DifferentialExpression

updated 3.0 years ago • Jayesh Kumar

look great. I it would be really nice to have all the 5' ends of the genes of interest begin on the left hand side of the track. Is there a way to simply "flip" this track (or any track for that matter) when potting using plotTracks

gviz gviz-package

updated 7.6 years ago • stephen.williams

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

seems* to work under 1.8.0, but you are welcome to report odd things you would notice). We made some recent changes in our code to try to speed it up (because it was slooooow, and still is), which hopefully did not introduce bugs...with the current release of 'affy' (version 1.2.x) and should work with the devel version too. The source for the package is available in the CVS section of Bioconduc…

affy affy

updated 22.3 years ago • Laurent Gautier

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 5.6 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 9.8 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

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...gt; Subject: RE:…

Microarray Category Microarray Category

updated 21.5 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

border="0" cellpadding="3" cellspacing="0" style="width:100%"> <tbody> <tr> <td> <table align="left" border="0" cellpadding="1" cellspacing="5"> <tbody> <tr> <td> <pre> Dear Bioconductors, I am delighted to announce a major re-release...of the EnrichmentBrowser package in line with its recent publication: Geistlinger L, Csaba G, Zimmer R.…

genesetenrichment functional enrichment enrichmentbrowser News

updated 9.9 years ago • Ludwig Geistlinger

Location: "http://www.bioconductor.org/data/dataL inks.html" <html><head> <title>Data Sources</title> <link href="../R.css" rel="stylesheet" type="text/css"/> <base target="main"/> </head> <body> <h3>Sources For Our Data Packages</h3> <ul

Annotation affy Annotation affy

updated 23.4 years ago • Johanne Duhaime

Hi,  I can't download WGCNA on Windows.  When I use command: <pre> source("http://bioconductor.org/biocLite.R") biocLite(c("AnnotationDbi", "impute", "GO.db", "preprocessCore")) install.packages("WGCNA...pre> I get following error: <pre> > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for h…

go.db WGCNA

updated 8.9 years ago • s3462450

<div class="preformatted"> D. Kulp of Affymetrix commented on the upcoming proprietary GeneChip data formats in a Bioconductor mailing list post of 25 June 2003. He notes that Windows/Java linkable libraries will be provided for reading the binary GeneChip format, and that MAGE/ML exports will be available. He proposes 1) Bioconductor can provide free compiled libraries using the API and …

Microarray GO Cancer cdf Microarray GO Cancer cdf

updated 22.5 years ago • Vincent J. Carey, Jr.

<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

except, as far as I can tell, its data was collected in 2009, which is rather a long time ago in the history of miRNA. I suspect more current version of the data would be pretty different from those generated in 2009. Am I mistaken...is a priblem, can you suggest a mechanism by which I might obtain more current predictions from many sources using Bioconductor? Best, Tom</div

miRNA RmiR miRNA RmiR

updated 12.1 years ago • Thomas Hampton

<div class="preformatted">Hi everybody, when trying to calculate the Toptable in affylmGUI there pops the following error message up: Error: The biocReposList() function is defunct. Please use biocLite() to install packages source("http://bioconductor.org/biocLite.R") biocLite("<pkgname>") if you really need to get the list of Bioconductor package repositories (like biocReposList() …

affylmGUI affylmGUI

updated 13.5 years ago • Burkhard Heil

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

div class="preformatted">Dear list, I had some doubts on the data sources used by athPkgBuilder that I post on bioc-devel list two months ago, but got no reply. I would like to try one more time...function in AnnBuilder (builder of ath1121501 and ag) and have some questions about the data source being used: 1. probeset id to gene mapping: The current mapping strategy was 1) map probe id to "…

Annotation Pathways GO probe oligo Annotation Pathways GO probe oligo

updated 19.4 years ago • Nianhua Li

<div class="preformatted">Dear Alessio and Gavin, Thanks for pointing out the problem with reading quantarray files. The bug has now been fixed in limma 2.9.1. limma now reads the annotation columns for quantarray files as well. Best wishes Gordon > Date: Wed, 4 Oct 2006 09:43:50 +0100 > From: "Gavin Kelly" <gavin.kelly at="" cancer.org.uk=""> > Subject: Re: […

Annotation Cancer limma Annotation Cancer limma

updated 19.3 years ago • Gordon Smyth

getProbeDataAffy', this is a function that works for the "normal" probe_tab files. Its (simple) commented source code is available through the source packages (.tar.gz). I recommend using this as a template and adapting...t include a Probe Interrogation Position since I > didn't have consensus sequence information - left all values for this column > zero) and compressed it in .gz fo…

cdf probe gcrma cdf probe gcrma

updated 20.4 years ago • Wolfgang Huber

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 21.5 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 want to using the VSN to process some data in C++ and where can I find the source code of VSN？ Please help me！ http://bioconductor.org/packages/release/bioc/html/vsn.html, Here is the homepage of VSN...I want to using the VSN to process some data in C++ and where can I find the source code of VSN？ Please help me！ http://bioconductor.org/packages/release/bioc/html/vsn.html, Here is the homep…

vsn r language C++ source code

updated 8.9 years ago • core_wzw

div class="preformatted">Hi, I tried to install R in my Linux using the source code from the mirror site. The latest is R-2.8.0.tar.gz. I unpacked and compiled the source code. However, when I tried...day 15 language R Wonder if anyone here has same problems before? Where do you guys obtain R source code? Thanks Johnny Li [[alternative HTML version deleted]] </div

updated 17.1 years ago • Li,Qinghong,ST.LOUIS,Molecular Biology