Bioconductor Forum

be generated for each set of genes tested for functional enrichment, one containing the enriched categories, and another containing the depleted categories (see .enriched and .depleted files). The .enriched file will contain...those categories that are found to have enriched representation among that set of genes. Similarly, the .depleted file will contain...those functional categories that are d…

go enrichment gene ontology goseq go

updated 6.3 years ago • Raito92

object produced by hyperGTest() function from "GOstats" package is the total size of a given GO category. In this regard I am puzzled why values in this field are slightly different for the same GO categories when I run the

GO Category GO Category

updated 16.9 years ago • Sergei Manakov

that also Genes with an NOT qualifier are annotated (roughly 3% of the fly genome) to a certain GO category making them indistinguishable from genes that are truely associated with a GO category.  Did I overlook something

org.dm.eg.db gene ontology go enrichment annotation NOT

updated 8.8 years ago • ivozeller

the transcript not compatible with either mature forms.Hence, for each microRNA transcript I have 3 categories. (I can actually define more categories since reads that are compatible with the mature forms often include modifications...nbsp; What I want to test is whether the proportions among the 3 categories mentioned above are affected by my experimental conditions (i.e., factors). Is…

voom limma glm multinomial regression

updated 9.4 years ago • rubi

div class="preformatted">HI, It appears that when colnames of the topTable output changed from "M" to "logFC", etc., the resort.by argument was not completely changed. The sort.by="M" and resort.by="A" arguments work...XML "2.6.0" "1.6.0" "1.8.0" "0.7-0" "1.4-0" GOstats Category genefilter survival KEGG "2.0.3" "2.0.3" …

GO Survival Biobase annotate genefilter affy affydata graph gcrma matchprobes annaffy

updated 18.8 years ago • Jenny Drnevich

its pity that your recent version does not work properly due to you have updated some functions and their arguments. \#\# changes in some functions...become "OrgDb". In enrichGO function: previous it was organism="zebrafish" " and now you changed into "OrgDb". Note: Anyway i made changes into my script but i found its not working at all. PLEASE HELP AND FIX IT ASAP. …

clusterprofiler

updated 9.1 years ago • unique379

on [www.ensembl.org](http://www.ensembl.org/index.html). If you are using biomaRt, you can change your host to access our most recent data (With R 2.2 and Bioconductor version 3.1) ensembl\_mart\_80 <- useEnsembl...domains start and end attributes (protein-based coordinate) A complete list of the changes in release 80 can be found at &l…

biomart Ensembl zebrafish Rat 1000 genomes phase 3 News

updated 10.6 years ago • Thomas Maurel

preformatted">Dear all, The new Ensembl marts for release 70 are live on www.ensembl.org. You can change your host to access our most recent data: mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path...Updated Human assembly to GRCh37.p10 and Mouse assembly to GRCm38.p1 A complete list of the changes in release 70 can be found at http://www.ensembl.org/info/web…

genomes genomes

updated 12.9 years ago • Thomas Maurel

if the effect of condition NN vs N in treatment S is different from that in treatment C, so I changed the design as below ```r design(dds) <- ~ treatment + condition + treatment:condition dds <- DESeq(dds) resultsNames(dds) "Intercept

DESeq2

updated 3.6 years ago • mmartinez

ComBat it has raised to 0.0722117750339454 How could be that a 0 value (no expression) has been changed to a higher value? How to avoid this behaviour? using 'mean.only = T' makes things even worse and a much higher number of

ComBat batch effect sva normalization

updated 6.7 years ago • hackingfactory

the parameters from all genes (incl. the differential ones) to a subset which are enriched for non-changing." In this context I have two questions: 1) What is the minimum number of genes/probes that should be used for VSN parameter...My apologies if this is trivial, my programming skills are still rather a disgrace :) ) Any comment on these questions would be highly appreciated. Kind regards,…

Microarray probe vsn Microarray probe vsn

updated 18.2 years ago • Stefan Thomsen

Hello, I have done DEXSeq test for my C, L, S three conditions samples and got the html report like below: I noticed that the log2 fold changes are caculated by the usage coefficient columns(c, l, s), but I am not clear that how those coefficients are caculated. I...C, L, S three conditions samples and got the html report like below: I noticed that the log2 fold changes are caculated by the us…

dexseq

updated 5.1 years ago • ywu

<div class="preformatted"> Hi again, First, I'd like to say thanks to everyone who's sent comments or suggestions on this. I've now managed to sort the problems out but just wanted to reply to a few of the questions raised...div class="preformatted"> Hi again, First, I'd like to say thanks to everyone who's sent comments or suggestions on this. I've now managed to sort …

GO probe PROcess GO probe PROcess

updated 21.8 years ago • Horswell, Stuart

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. Bioconductor's EnrichmentBrowser: seamless navigation through combined...Bioinformatics, ISMB/ECCB 2011), and novel ways of combining and exploring results across methods. Comments and suggestions to further improve the EnrichmentBrowser ar…

genesetenrichment functional enrichment enrichmentbrowser News

updated 9.9 years ago • Ludwig Geistlinger

div class="preformatted">Dear all, this is to summarise recent changes to the "vsn" package that might be of interest: * In addition to normalising a set of arrays against each other, it

Classification vsn Classification vsn

updated 18.8 years ago • Wolfgang Huber

div class="preformatted"> With a recent update of bioconductor it appears to me that a little bug has been introduced into plotMA() in the limma package: Selecting...with plotMA(foo, array=2) does not work anymore if foo is an RGList. The reason seems to be a small change in the respective part of the source code from MA <- MA.RG(MA[, array]) array <- 1 in limma 2.12.0 (2…

limma limma

updated 17.6 years ago • Philipp Pagel

<div class="preformatted">Hi Daniel, [cc'ing our mailing list] Thanks for the report! This is fixed in the release (1.8.4) and devel (1.9.12) versions of IRanges. Both should become available via biocLite() in the next 24 hours. Cheers, H. On 11/25/2010 06:38 AM, Daniel Nebdal wrote: > Hi. I recently tried to install IRanges (both the stable and devel > versions from bioco…

Cancer IRanges Cancer IRanges

updated 15.1 years ago • Hervé Pagès

<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

new Ensembl marts for release 98 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart98 <- useEnsembl(biomart=“ensembl") Important: Please note that

biomart ensembl e98 mart News

updated 6.3 years ago • Thomas Maurel

for your email and noticing the error. A parameter of the glmnb.fit function (statmod package) changed recently from "start" to "coef.start". That was making some problems in DEXSeq, but I adapted the DEXSeq code to it. Could

DEXSeq DEXSeq

updated 13.4 years ago • Alejandro Reyes

18, 2005 10:16 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] R-2.2 and BioConductor 1.7: changes in GC-RMA and fitPLMprocedures Hello, I submit this message to the mailing list because I think that more people encounter...and perform the separate required steps in a new script). Unfortunately, in BioC 1.7 things has changed significantly in such a way that it is more difficult to do…

Normalization Normalization

updated 20.2 years ago • Groot, Philip de

the following, sce <- loadHDF5SummarizedExperiment("original_data/") ## make lots of changes to big dataset sce ## ## maybe something computationally nasty that can't be 'delayed'? sce2 <- saveHDF5SummarizedExperiment

HDF5Array

updated 6.9 years ago • sarah.williams1

values are calculated based on only those genes assigned to any GO term. In my case, i have only one category, so it is expected that there are genes not assigned to any of "my" categories. Is their usage (therefore setting `use_genes_without_cat

goseq

updated 6.9 years ago • kubovcij

t find them...)...Maybe, there are trivial solutions... First, how I can find all the different GO category associated with a locus identifier ? Second, is it possible to reverse the previous question, that is to find all the...locus associated to a GO category ? Thanks a lot for your help... Best regards, Olivier. </div

GO GOstats Category GO GOstats Category

updated 19.3 years ago • Martin Olivier

mikelove/DESeq2/blob/d5e6e09e33d7cdafc64f55a44bdcad94812569b7/R/helper.R#L98) from GitHub and changed line 98 to method="L-BFGS-B", lower=c(.0001,.0001),upper=c(Inf,Inf))$par The function now worked for me. Of course now all values...sense. Just wanted to report this because I'm not a statistician and don't know if this could have changed my output in any significant way. If not this might…

deseq2 unmix

updated 7.1 years ago • a.v.vliet

when I went to re-run it I now get the following two errors. Did the behavior of these functions change? I'd like to take the range of exons in a gene (union of all isoforms) and define everything in between as introns. I'd also

genomicranges

updated 8.8 years ago • Jake

significant under class1 > class2 (Down >> regulated >> genes). When I see the fold change value in both tables , there are >> some >> genes having fold change value less than 1 in Table 1 and some genes >&gt...have >> fold change value greater than 1 in Table 2. >> "If the Gene has fold change v…

Cancer probe RankProd Cancer probe RankProd

updated 16.1 years ago • Fangxin Hong

fails. I didn't have much luck so far with my attempts to work around this: 1. Trying to change the signature of the c() generic: > setGeneric("c", signature="...") Error in setGeneric("c", signature = "...") : ?c? is a primitive function...methods can be defined, but the generic function is implicit, and cannot be changed. 2. Trying to dispatch on "mis…

Cancer IRanges BiocGenerics Cancer IRanges BiocGenerics

updated 13.1 years ago • Hervé Pagès

May 1, 2012 2:28:29 PM GMT+02:00 > To: bioc-devel at r-project.org > Subject: [Bioc-devel] Changes in the %in% function for DNAStringSet? > > Hi all, > > In R 2.15.0, Bioc 2.10, the following works: > > library(Biostrings...not attached): > [1] stats4_2.15.0 > > > > I'd just like to know if that is that a c…

updated 13.7 years ago • delhomme@embl.de

Let's say I store the 4 batch labels in DBA_TISSUE. The following: data = dba.contrast(data, categories=DBA_CONDITION, block=DBA_TISSUE) returns the following warning messages: Warning messages: 1: Blocking factor...contrast via mask (for example BATCH_1 VS !BATCH_1) this works correctly: data = dba.contrast(data, categories=DBA_CONDITION, block=data$masks$BATCH_1) however it will only block…

updated 11.5 years ago • Giuseppe Gallone

I changed the color palette from the dba.plotPCA very easily: I defined mypalette=c() (whatever colors I want) and then dba.plotPCA

DiffBind plot color

updated 6.0 years ago • melnuesch

The change in 2.4.0 was introduced to better handle the possibility of residual standard deviations being exactly zero. The...discussion from the Bioconductor mailing list at that time. Later I became worried that the above change would make limma slightly more conservative and would change people's historical results. So in 2.4.13 I wound it back...45 (out of 15000) DE genes >(with a p-v…

Microarray limma Microarray limma

updated 19.7 years ago • Gordon Smyth

the actual keyword value starts with <delimiter_char> For example: "|$COM||| Delimiter starts my comment|" (| is the <delimiter_char> in my examples) 2) <delimiter_char>x where x is not a <delimiter_char> means that the vendor broke...simply means that the keyword value is starting with character x. For example: "|$COM|My comment|" It goes down to the question whether it…

Cancer safe flowCore Cancer safe flowCore

updated 13.5 years ago • Josef Spidlen

version from x.y.z to x.y.(z+1) in your package’s DESCRIPTION file. If the version is not properly changed your changes will not be made available in the Bioconductor public repository. 4) Now build your package tar ball with...pre> R CMD build geneXtendeR</pre> 5) Now check that the changes have produced a package consistent with R’s check facility: <pre> R CMD check geneXten…

subversion bioc-devel package development usedevel Tutorial

updated 8.4 years ago • Bohdan Khomtchouk

lt;- model.matrix(~0+genostage) Now, I would like to define the contrast to determine changes in expression over time (developmental stage) between two genotypes. According to examples in the limma manual

limma

updated 8.9 years ago • j.baldauf

On Wed, 3/12/14, Ashesh wrote: Dear Dr. Luo, I recently performed some RNA-seq experiments and want to use the Pathview software to look at changes in biological pathways...Since, I am a beginner I have not been able to determine how best to resolve this error. ?Should I change the bam file header? ?Is there a way to modify the TxDb.Hsapiens.UCSC.hg19.knownGene file? ?Is there a work aro…

Pathways pathview Pathways pathview

updated 11.8 years ago • Luo Weijun

equivalent to _glmTreat() _in multiple factor experiments to use to get DE genes relative to a fold-change of 2 or similar? &nbsp

edgeR deanalysis test fisher exact

updated 7.8 years ago • tkapell

other two parameters, but it should be independent of these parameters. Thank you very much for your comments and help! (and your patience) Jordi Altirriba IDIBAPS - Hospital Clinic (Barcelona, Spain) > >Hello Jordi, > >My comments...p=0.1) [[1]] > >mainDIgenes<-sapply(lm.f.Fsub, FUN=mainES) > >##### ># See above comments. &am…

multtest limma factDesign multtest limma factDesign

updated 21.7 years ago • Jordi Altirriba Gutiérrez

there was a new release of Ensembl (This usually happens every two months). Normally there are few changes in attribute names, however there were some attribute name changes in this release. Use the command below to get all...exon_chrom_end and exon_chrom_start do get what you want. Cheers, Steffen > listAttributes(mart,category="Structures") name 1 …

biomaRt biomaRt

updated 17.4 years ago • steffen@stat.Berkeley.EDU

result for me, I tried my library with both of the normalization methods. I characterized log(fold change) > 1 and p-value <0.05 as "positively enriched peaks", and log(fold change) < -1 and p-value<0.05 as "negatively enriched...filename) atac.count <- dba.count(atac.list) atac.contrast <- dba.contrast(atac.count, categories=DBA\_CONDITION, block=DBA\_…

diffbind Deseq2 edger differential binding analysis

updated 8.1 years ago • ew152

mailling list, and hacked as much of the internal functions as I am able -- how does lumiMethyR change the raw values from the input file? I noticed that when I extract values using "exprs", I get different raw methylation...gt; m2beta(exprs(mlmdat)[1:4,1]) mlmdat is of the class "MethyLumiM" And I noticed that this change occurs in the second line of the "lumiMethyR" function, when the "MethyL…

Normalization probe lumi Normalization probe lumi

updated 10.9 years ago • Nick Fishbane

gt; From: "michael watson $IAH-C$" <michael.watson at="" bbsrc.ac.uk=""> > Subject: Re: [BioC] Change M-value calculation from red/green to > green/red > To: "Torsten Waldminghaus" <torsten.waldminghaus at="" rr-research.no...gt; Sent: 10 June 2009 10:59 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Change M-value calculation from re…

Microarray Normalization Cancer limma Microarray Normalization Cancer limma

updated 16.6 years ago • Gordon Smyth

Is there a way to change the font size of the annotation axis values? These values often overlap, is the sizing automatic (circled in red below

ComplexHeatmap

updated 3.5 years ago • nalaspina

<div class="preformatted">The limma package has a new function topTableF() which ranks genes by F-statistic. I am planning to add a feature to topTable() to access ranking by F-statistic. At present, topTable(fit, coef=c(2,3,4)) would be an error. In future, this will rank genes by the F-statistic for the 2nd, 3rd and 4th coefficients of fit. At present the default value for 'coef' i…

limma limma

updated 19.3 years ago • Gordon Smyth

a deeper understanding of the molecular mechanisms of cancer and its response to therapies. Recent studies of tumor cellular sub-populations have revealed that many human tumors are composed of multiple mutated...of intra-tumoral heterogeneity provides an important genetic reservoir allowing tumors to adapt to changing environments or therapeutic selection pressures. Since the mechanisms that dr…

cancer genomics postdoc job Job

updated 9.7 years ago • Kauffmann, Audrey

for each gene remained unchanged between (1) and (2), which is as expected. However, the F statistic changed, tend to be decrease, for some genes. As a result, genes identified as significant (FDR < 0.05) in (1) would become in-significant

glmQLFTest edgeR

updated 3.6 years ago • Pei

My data are log2 fold changes (FCs) between control and treatment usually coming from triple replicated affymetrix microarrays. I also have p...My data are log2 fold changes (FCs) between control and treatment usually coming from triple replicated affymetrix microarrays. I also have p-values

limma logfc lmfit

updated 10.6 years ago • Moritz E. Beber

Import data to DESeq2 with tximport 3. Identify differential expression with a (varying) log-fold change using apeglm, resulting in S-values and a significance threshold of 0.005 was applied. We have repeated this experiment...species using the same R code, and in one of the species the MA plots indicate a tiny amount of fold-changes for the majority of genes in the experiment; this is true …

deseq2

updated 6.7 years ago • Jack.Hearn

control and knock-down for each cell line in triplicate. We would like to find the gene expression changes due to knock down that are __common __across the three cell lines. <pre> > dds <- DESeqDataSetFromMatrix(countData...cell.line_B_vs_A" "cell.line_C_vs_A" "shRNA_kd_vs_scr" > results(dds) log2 fold change (MLE): shRNA kd vs scr Wald test p-value: sh…

deseq2 differential gene expression

updated 8.2 years ago • jason.wray

my data (which may be a bad idea to begin with..?), and would like to be able to use the GO slim categories to annotate my data (see http://www.spatial.maine.edu/~mdolan/MGI_GO_Slim.html), instead of the extremely detailed...GO categories already present in the affymetrix file - Gene.Ontology.Biological.Process, Gene.Ontology.Cellular.Component

Annotation GO annotate affy Annotation GO annotate affy

updated 20.9 years ago • Ken Termiso

about the locations of probes relative to 3' end and suppose the distances from 3' fall in 2 categories (X,Y). I am searching for a code that will enable me to partiotion probe-effect on the basis of the distance categories

probe probe

updated 22.2 years ago • Stephen Nyangoma

Because of the variability involved in patient samples, I expect that some gene expression changes after a given treatment, while they may be changing in the same direction (i.e. they are up-regulated in all treatments...vs controls within a patient sample) are not going to be consistent in the magnitude of change from patient sample to patient sample. Indeed, when I look at my normalized counts …

deseq2

updated 5.9 years ago • jropa

<div class="preformatted"> Hello list, My name is Makis, I am a bioinformatics post-doc fellow and, recently, I started working on a CAGE project. I am new on the field and trying to figure out some things, so I would much appreciate any comments on my problem. I am sorry if my question sounds a bit confusing... I have a Treatment vs Control (independent samples) experimental...div class=…

Transcription Annotation convert edgeR DESeq Transcription Annotation convert edgeR DESeq

updated 13.3 years ago • Makis Motakis

that is not. When looking at my MA Plot it appears that there are man genes that have a log2 fold change > 2 , in my rank it shows that there are only 11 such genes. Has anyone else experienced this problem? Here is my code for...both the rank list and MA plot if that is helpful:  \# order by Fold Change - Rank List rankList = as.data.frame(results\[order(abs(results$log2FoldC…

deseq2 rna-seq

updated 10.5 years ago • ejmcmaho

seizure history yes group, I would like to take one individual from the group, calculate log2 fold change against all individuals in no seizure history group. In other words, I am calculating log2fold change of gene expression

deseq2 L2FC log2fc

updated 8.4 years ago • sup230

div class="preformatted">Dear all, I am using limma to perform differential analysis between two categories. Some samples in my set do not fall in either category. I can see that there is two ways to approach this: 1) Set the non...category samples to zero in the design matrix e.g. > design Low High GSM89690 0 1 GSM89724 0 1 GSM89728 0 0 GSM89737 0 1 GSM89…

Cancer limma Category Cancer limma Category

updated 18.4 years ago • Daniel Brewer

samples based on a sample QC criteria we have found effective. Unfortunately, none of these handy changes are yet detailed in the vignette; we are working on this. A manuscript is in review detailing most of these functions...Best, Kasper D Hansen o Added getMethSignal(), a convenience function for programming. o Changed the argument name of "type" to "what" for getMethSignal(). …

SNP Annotation minfi bumphunter SNP Annotation minfi bumphunter

updated 12.1 years ago • Kasper Daniel Hansen

is calculated in this case ; I also do nto really understand the sentence " Note that the log2 fold change for treatment of OHT over control for patient 4 is the interaction effect above in addition to the main effect of treatment

DESeq2 DESeq2

updated 11.6 years ago • samuel collombet

Hello, everyone! I recently encountered an interesting problem that I [asked][1] the Bioinformatics Reddit about, which elicited a split opinion...Eppendorf tubes to perform RNA-sequencing. **Question**: If I am most interested in exploring the changes in genes between the upstream and downstream for each stenosis condition (e.g. 70% stenosis downstream vs. 70% stenosis...downstream. Many thanks…

DESeq2

updated 8 weeks ago • Alexander

Hi all, First post here, so apologies if I haven't explained anything clearly/followed standard guidelines. I'd like to create a summarized experiment object for downstream analysis of my count data from RNA seq analysis.  The way I do this is something like this: rna_raw_counts_no_tech_rep_ordered.se <- SummarizedExperiment(list(rna_raw_counts_no_tech_rep_ordered), r…

deseq2 summarizedexperiment rangedsummarizedexperiment rnaseq

updated 8.7 years ago • krc3004