Bioconductor Forum

div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only.</div

updated 22.5 years ago • madman@jimmy.harvard.edu

div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only.</div

updated 21.5 years ago • madman@jimmy.harvard.edu

div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 30 April 2004: annaff…

GO annaffy GO annaffy

updated 21.6 years ago • madman@jimmy.harvard.edu

div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 08/06/2004 The bug…

probe probe

updated 21.4 years ago • madman@jimmy.harvard.edu

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Annotation Annotation

updated 22.4 years ago • madman@jimmy.harvard.edu

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limma limma

updated 21.4 years ago • madman@jimmy.harvard.edu

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Annotation GO Biobase Annotation GO Biobase

updated 22.1 years ago • madman@jimmy.harvard.edu

div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 5 July 2003: limma - …

limma limma

updated 22.4 years ago • madman@jimmy.harvard.edu

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affypdnn affypdnn

updated 21.3 years ago • madman@jimmy.harvard.edu

div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 6 Dec 2003: limma 1.3…

limma limma

updated 22.0 years ago • madman@jimmy.harvard.edu

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reposTools graph widgetTools limma reposTools graph widgetTools limma

updated 22.2 years ago • madman@jimmy.harvard.edu

div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 7 April 2004: limma 1…

probe reposTools limma probe reposTools limma

updated 21.7 years ago • madman@jimmy.harvard.edu

div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 05 Feb 2004: reposToo…

reposTools graph Rgraphviz simpleaffy impute reposTools graph Rgraphviz simpleaffy impute

updated 21.9 years ago • madman@jimmy.harvard.edu

div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history...REL1.1 and Devel) - JG Apr 29 2003: annotate - references to data package hgu95a have been changed to hgu95av2. JG Apr 29 2003: limma - imported version 1.0.2 - fixed bug in ebaye…

Normalization hgu95a hgu95av2 annotate reposTools limma Normalization hgu95a hgu95av2

updated 22.6 years ago • madman@jimmy.harvard.edu

<div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 06 September 2003: …

genefilter affy graph Rgraphviz limma annaffy genefilter affy graph Rgraphviz limma

updated 22.3 years ago • madman@jimmy.harvard.edu

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Microarray Ruuid graph limma EBarrays Microarray Ruuid graph limma EBarrays

updated 21.8 years ago • madman@jimmy.harvard.edu

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SAGE annotate geneplotter graph SAGElyzer Rdbi SAGE annotate geneplotter graph SAGElyzer

updated 22.9 years ago • madman@jimmy.harvard.edu

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limma Rintact limma Rintact

updated 21.9 years ago • madman@jimmy.harvard.edu

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MultiChannel tkWidgets affy Rgraphviz MultiChannel tkWidgets affy Rgraphviz

updated 22.8 years ago • madman@jimmy.harvard.edu

Hi Matt and Nadia, For almost a year, I was using goseq as a generalized enrichment tool (leveraging the gene length bias correction implemented there, thank you) using my custom gene sets this way: goseq(myData, genome=NULL, id=NULL, gene2cat = MyVeryOwnGeneCategorization, method="Sampling", repcnt = 100000) After recent update to version 1.18.0, the pipeline crashed and return…

goseq

updated 10.9 years ago • Oleg Moskvin

the changes in expression not explained by the cell counts (either because they come from cell types not included in the model...and platelets). - Some possible confounding variables (age, sex, running time). - 3 categories (more or less uniform), each category is characterized by the distance of the race (14km, 35 km and 55 km). ### Alternatives...GEbefore** **deltaCell = (CellAfter …

limma model selection several covariables pre-post whole blood

updated 5.7 years ago • p.figuerola.9

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Biobase Ruuid DynDoc tkWidgets affy graph Rgraphviz AnnBuilder RBGL PROcess Biobase

updated 22.7 years ago • madman@jimmy.harvard.edu

div class="preformatted">Hi all, I recently came across a paper (Maria Chahrour, et al. MeCP2, a Key Contributor to Neurological Disease, Activates and Represses...Figure S1 which basically plots cellular component, biological process, and molecular function categories that differ significantly based on on genes that are differentially expressed in two conditions. I wonder whether

updated 17.6 years ago • affy snp

<div class="preformatted">Dear list, I have a theoretical question regarding Filtering on Variation in the Category package. I've performed an analysis that closely resembles the Vignette, but I am still a bit uncertain about the filtering...<div class="preformatted">Dear list, I have a theoretical question regarding Filtering on Variation in the Category package. I've performed an …

updated 18.4 years ago • Boel Brynedal

everybody, I was wondering whether there is a package to cluster a list of genes to different GO categories my problem is as such: i have a list of genes (a tab delimited file): id flybasename_gene flybase_gene_id entrezgene...FBgn0034454 37248 protein binding I would like to try and group the genes in various GO categories, which are mentioned here in the last columns. The GO c…

Annotation GO Annotation GO

updated 15.0 years ago • Assa Yeroslaviz

I can't change the y-axis' category order of dotplot result, I don't know the default order of it. I've used ordrBy="x",orderBy="Count",orderBy...I can't change the y-axis' category order of dotplot result, I don't know the default order of it. I've used ordrBy="x",orderBy="Count",orderBy="geneRatio" in dotplot() parameters, but nothing changed. Thank you very much! ``` #ego <- enric…

GO.db clusterProfiler dotplot barplot

updated 4.2 years ago • Yang

Dear all, I have some gene expression data sets. In some of the data sets, I am comparing two age categories, and in some I am comparing multiple age categories. For each dataset, I want to do a two-tailed F test between the age...me. I'm really struggling and I just don't understand specifically where in the code I am meant to change; I didn't want to keep bothering Dr. Ryan, so I emailed Prof.…

limma f test differential gene expression

updated 9.1 years ago • StephK

expression (lmFit and eBayes). I get a high number of DE genes. Most of these belong to Category: Main. However, some of them, belongs to other categories such as normgene->intron, control->affx, normgene->exon...As I understand it, empirical Bayes takes into consideration the full data set. Removing all other categories, some of them which are not supposed to be changed bet…

limma plier oligo limma plier oligo

updated 13.4 years ago • Martin O'Hare

div class="preformatted">Hi, I am having troubles with cateGOry as follows: > m <- cateGOry(go$refseq_dna, go$go, FALSE) Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442...Neither worked. Any idea? Thanks, Oleg > index <- c(24, 172, 1978, 1979, 4441) > m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE) Error in augment…

GO Category GO Category

updated 18.6 years ago • Oleg Sklyar

This is a request for comments on planned changes to the ensemblVEP package. The intent is to provide lightweight wrappers to the ensembl VEP REST...API and to deprecate most of the software in the package. Users of ensemblVEP may respond with comments to this post to describe their use cases. As examples of new approaches emerge in development, I will post more details

VariantAnnotation ensemblVEP

updated 23 months ago • Vincent J. Carey, Jr.

div class="preformatted">What follows is some random comments on the use of GRanges for storing data in the elementMetadata slot. My use case is a lot of very small ranges (>10M...but very important to me :). I am particular interested in fast subsetting like subsetByOverlaps. Comments: * I find column subsetting on the elementMetadata to be really slow, slower than it need to be I …

updated 15.3 years ago • Kasper Daniel Hansen

go to http://www.bioconductor.org/help/course-materials/ (also accessible from our home page as the "Recent courses" link in the "Learn" box) Courses are searchable and sortable by keyword, course name, title, date, and more. Thanks...to everyone who attended BioC2014 and gave us feedback which prompted this change. Dan

course-material News

updated 11.3 years ago • Dan Tenenbaum

<div class="preformatted">Hello bioC users, as you can see below, this was posted over a year ago. Unfortunately I tried the same today and for some mysterious it is not working correctly any more. What I have is the same data.frame: > dat id flybasename_gene flybase_gene_id entrezgene 1 1616608_a_at Gpdh FBgn0001128 33824 2 1622892_s_at CG3…

GO GO

updated 13.3 years ago • Assa Yeroslaviz

the best way to proceed in this case. "Level1" individuals become "level2" individuals because they change behavior throughout their lifespan. Perhaps that "level2" individual had very recently transitioned from "level1...that "level2" individual as "level1", or perhaps consider "level1 + level2" individuals as a single category and compare against "level3", since I'm mostly interested in the gen…

deseq2 DESeq2

updated 7.5 years ago • fl

I had written to do GO analysis using the package GOstats, and to do this by switching to package Category. I wanted to add KEGG testing to the GO testing I have been doing. All I did to my code was to add a conditional such that...if the category was KEGG a KEGGHyperGParams object would be created, else if it was BP, MF, or CC a GOHyperGParams object would be created...Then the object params wou…

Annotation GO GOstats Category Annotation GO GOstats Category

updated 17.8 years ago • Mark W Kimpel

div class="preformatted">Hi, Instead of using GO or KEGG categories, is it possible to use customerized categories. For example: CC1 : gene1, gene2, gene3 CC2 : gene4, gene5.. instead of GO1...gene1, gene2 I am just wondering which package allows me to give my own defn. of categories. For this purpose, I made a code from basic Hypergeometric {stats} by using dhyper. But what I got is prob…

GO GO

updated 19.0 years ago • Weiwei Shi

shorter lines; 501 lines (14%) are > 80 characters long. Most of these lines are roxygen comments. formatR package says : > Also note that single lines of long comments will be wrapped into > shorter ones automatically...when wrap = TRUE, but roxygen comments will > not be wrapped (i.e., comments that begin with #'). Don't tell me I have to do this one l…

BiocCheck

updated 4.3 years ago • ZheFrench

bosTau4", "ensGene") > GO.hiper = goseq(pwf, "bosTau4", "ensGene") > GO.hiper[GO.hiper$category=="GO:0005509",] category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology...182</strong> calcium ion binding MF</pre> Even if I force the inclusion of genes without categories in the test, the number of genes per category is th…

goseq biomart

updated 7.5 years ago • frezende

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]

if I type a function name in R, it'll print the function for me. Unfortunately, it does so without comments. Is there a way to get the function with comments? A related question: how can I access the documentation/comments for

cdf cdf

updated 17.5 years ago • Arkady

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

  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

Is there a simple way to get comments from a VCF header of a VCF object? For example, consider the following excerpt of a VCF file: ##contig= <id=hla-drb1*15:03...Is there a simple way to get comments from a VCF header of a VCF object? For example, consider the following excerpt of a VCF file: ##contig= <id=hla-drb1*15:03:01...1] "VariantAnnotation" header(header(varian…

VariantAnnotation VCFHeader

updated 5.5 years ago • Dario Strbenac

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

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

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 4.7 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

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 10.8 years ago • Michael Love

nbsp;ConB  ConB  ConB  Levels: ConB CondA what can I understand from log2fold change. does it mean that a gene from condA is higher when it is positive and or lower when it is negative  in regards to conB...gene, a log2 fold change of -1 for `` condition treated vs untreated `` means that the treatment induces a multiplicative change in o…

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 19.6 years ago • Srinivas Iyyer

Mon, 12 Mar 2007 14:39:54 -0700 From: "Lana Schaffer" <schaffer@scripps.edu> Subject: Re: [BioC] Category To: <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <016001c764ee$f92bf4b0$54508389 at menton> Content-Type...want to put the GSEA curated databases(Broad Institute) into R so that they can be used by the Category program. I need more disease states than what …

Category Category

updated 18.8 years ago • Simon Lin

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