Bioconductor Forum

preformatted">Dear all, The new Ensembl marts for release 74 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...somatic datasets. Added new variation species sheep (Ovis aries) A complete list of the changes in release 74 can be found at http://www.ensembl.org/info…

updated 12.1 years ago • Thomas Maurel

Hello -  I have run a dba analysis on 4 cell types, each with 2 replicates. The way I've setup the call to dba.analyze  results in 10 contrasts. I have two questions about retrieving the results: 1) Is it possible to retrieve the DB peaks from an individual contrast, with the score column reported for all samples, in RPKM? The code I've used is pasted below. It retriev…

diffbind

updated 9.8 years ago • JD

default values in aveLogCPM() and with the DGEList method for plotMDS()</pre> I agree with this change, but I wanted to point out that the default value for prior.count should also be changed in glmFit() from 0.125 to 2 so that...the fold-change estimates better match the logCPM values. I noticed a while ago that for genes with very low aveLogCPM that the reported...log fold-change esti…

edgeR prior.count

updated 7.2 years ago • Jenny Drnevich

Hi, I am using Zebrafish Gene 1.1 ST Array Strip from Affymetrix. Affymetrix categorizes the transcript clusters as: main - part of the main design control->affx - a standard AFFX control control->chip - a chip control control->bgp->antigenomic - contains antigenomic background probes control->bgp->genomic - contains genomic background probes normgene->exon - from an exonic…

Normalization zebrafish Normalization zebrafish

updated 12.3 years ago • Joao Sollari Lopes

<div class="preformatted">Hi, I recently upgraded edgeR from 3.0.8 to 3.2.3 and I'm noticing some differences. I have some data that I normalized with EDASeq. I attempted to calculate the trended dispersion and I get the following error: > dglmtrend=estimateGLMTrendedDisp(exprs(dataNormgcOff),design,offset= -offst(dataNormgcOff)) Error in t(y) + prior.count.scaled : non-conformab…

edgeR EDASeq edgeR EDASeq

updated 12.6 years ago • suzy.stiegelmeyer@syngenta.com

it if you, or someone on the list could could clear up this problem) I am noticing a large change in the absolute values of intensity measurements For the same probeset and and array normalized with the same 8 other...arrays done with GCRMA 2.10 I got 5.27 but for GCRMA 2.12 I got 3.14 Does this sound like a change that can be expected between versions 2.10 and 2.12, or does …

Cancer gcrma Cancer gcrma

updated 17.5 years ago • Richard Friedman

div class="preformatted">I recently tried to install the iFlow flow cytometry GUI on top of my R/Bioconductor installation, and received a warning message...gt; source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). > biocLite("iFlow") Using R version 2.12.1, biocinstall version 2.7.4. Installing Bioconductor

GUI iFlow GUI iFlow

updated 14.9 years ago • Gabriel Nathan Kaufman, Mr

div class="preformatted">Dear Gordon and BioC users, I have recently updated R and BioC packages (R.2.3.0 and limma 2.7.9) and found the following issue when I try to subset a MArrayLM...at least for me). If this new behavior is limma's responsability, and not R's, may I suggest to change things in orther to allow subsetting using all contrasts again? Thanks Best Ariel./ </div

limma limma

updated 19.4 years ago • Ariel Chernomoretz

status ------ This might be due to a wrong hard coded kegg ftp path inside of KEGGgraph, as the recent integration of biopax files has changed the structure of the ftp://ftp.genome.jp/pub/kegg/xml/ directory. This has destroyed

KEGGgraph KEGGgraph

updated 15.8 years ago • Ludwig Geistlinger

fetch/56276’ cache path: ‘C:/.../AppData/.AnnotationHub/56276’ reason: Server denied you to change to the given directory

annotation annotationhub

updated 6.7 years ago • bastien.ducreux

Connolly sees this enough to have a standard message he sends out and Martin Maechler commented on it in the past, perhaps other Windows users of Outlook are doing the same thing I did. Rest assured that I have learned...I > sent one email to myself with the subject "test1" and then replied to it > without changing the subject. The reply correctly went to "test1" in the > inb…

updated 18.9 years ago • Kimpel, Mark W

My understanding from Sections 2.12 and 4.4.8 of the edgeR User's Guide is that the log2 fold changes for each gene will be tested against the absolute value of glmTreat()'s lfc parameter, which would output differentially

edger

updated 9.6 years ago • le2336

run as part of the nightly builds, but it is run several times a week. Only packages whose code has changed since the last calculation are run through covr. We hope this shield motivates package developers to add unit tests...web/packages/covr/README.html) for more information on how to do this. Questions and comments are welcome as always on the bioc-devel list. Thanks, Dan

test coverage News

updated 10.5 years ago • Dan Tenenbaum

untreated anymore and there will be no log2FC between them. Most lab people like to have fold change values. My questions: 1. Is it possible to stick with the  treated v. untreated groups here but get a clearer picture...measure could be used to justify this choice and the number of bins when bins are preferable? Any comments on the approach in general and how to actually analyze this …

deseq2 edger dose rna-seq

updated 10.2 years ago • JacobK

<div class="preformatted"> >To: "Giulio Di Giovanni" <perimessaggini at="" hotmail.com=""> >From: Naomi Altman <naomi at="" stat.psu.edu=""> >Subject: Re: [BioC] How to Change labels to a print-tip boxplot ? >Cc: >Bcc: >X-Eudora-Signature: <work> >Date: Mon, 20 Mar 2006 13:22:54 -0500 > >boxplot(MAset...hotmail…

limma limma

updated 19.8 years ago • Naomi Altman

I'm trying to understand the results of the AUCell run. I tested my single-cell data set with specific DC cell-types gene sets. The image below shows two fo the 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 expre…

AUCell

updated 3 months ago • gogeni5529

to estimate what kind of pseudocounts to use and I'm getting strange results with small number of categories: x<-c(312,14491,16401,65124,129797,323321,366051,368599,405261,604962) y<- goodTuring(x) y $count [1] 312 14491 16401...this properly, y$proportion is telling me that I should expect all my counts to fall under the last category, which does not make sense. I would expe…

Category edgeR Category edgeR

updated 13.4 years ago • Francois Pepin

> Date: Thu, 7 Sep 2006 07:38:33 -0700 (PDT) > From: "D.Enrique ESCOBAR ESPINOZA" > Subject: [BioC] X11 problem > To: bioconductor at stat.math.ethz.ch > Message-ID: <20060907143834.3932.qmail at web30503.mail.mud.yahoo.com> > Content-Type: text/plain; charset=iso-8859-1 > > i m running R in a fedora core 5 x86 server wothout > X11 service. > X11 is the defaul…

updated 19.3 years ago • Ross Lazarus

xlim = c(-2,2), ylim = c(0,6), xlab = bquote(~Log[2] ~ "fold change"), ylab = bquote(~-Log[10] ~ italic(P)), axisLabSize = 12, title = paste("NanoString -",data.name), subtitle = '', labFace = "bold", pointSize = 2, labSize

EnhancedVolcano

updated 3.5 years ago • junli1988

Hi everyone, I recently want to update the R packages 'xcms' and 'MSnbase' through following BiocManager command. BiocManager::install("xcms...now, I just manually download the tgz file to install the latest version. Can anyone provide any comments? Thanks, Lingjue **Thanks for the critic and answers. I fixed the issue by updating R version (3.5.3 -> 3.6.1) for latest

debug BiocManager R pacakge R mass spectrometry

updated 6.2 years ago • wang.lingjue

div class="preformatted">Dear Pekka, Thanks for your comments and for your interest in the camera procedure. In general, it is not possible to run the camera() or roast() procedures...lt;- camera(...) write.table(out, file="cameraresults.txt") Would that satisfy your needs? In recent limma releases, we have modified mroast() to give output as a data.frame, so that the format is more lik…

Microarray limma Category CAMERA GSVA Microarray limma Category CAMERA GSVA

updated 12.2 years ago • Gordon Smyth

to a pvalue using the normalized array data directly and then shows the differences as log2 fold changes in the top table? If you know the proper thered to refer to, that will be of great help, else, I am grateful for your responses

limma pvalue log2fc log2

updated 9.8 years ago • serpalma.v

for a number of feature/contrast combinations that I have a significant p-value, but the log2 fold change is reported as zero. How is that possible? How do I interpret this result? ![results spreadsheet][1] [1]: https://i.ibb.co/SBDcpmX

deseq2

updated 5.3 years ago • jennifer.weinert

gt;of some kind, in this case cancerous and normal, and the actual values >assigned to the categories are nominal. Have you read the LIMMA User's Guide? >The reason I asked about control spots refers back to an earlier...arrays >using negative controls. I don't know what you have in mind here. Have you followed the recent series of emails on using weights? > I do …

Microarray limma Microarray limma

updated 22.4 years ago • Gordon Smyth

I recently rewrote my R code so that it can be used with new dataset. In doing so, I changed the nomenclature of my sample Groups...I recently rewrote my R code so that it can be used with new dataset. In doing so, I changed the nomenclature of my sample Groups (used in Design). For some reason, the "Control vs. Treated" comparison is now being made, instead of the intended "Treated vs. Contro…

DESeq2

updated 4.8 years ago • vanbelj

div class="preformatted">dear all, recently I tried old scripts running siggenes function. to have reproducibility with sam in excel I used the option lambda...0.5. now it seems that with siggenes 1.20.0 this option is not available. did it simply changed the name, or it was removed? furthermore if I run the summary I am not conviced by the FDR calculation. as you can see, using...for the …

GO hgu133a siggenes GO hgu133a siggenes

updated 16.1 years ago • John Lande

e!83) has been released: <http://www.ensembl.org/> 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\_83 <- useEnsembl...Human assembly updated from GRCh38.p3 to GRCh38.p5   A complete list of the changes in release 83 can be found at <ht…

ensemble mart ensembl biomart ensembl release News

updated 10.1 years ago • amonida

website. This commands used to work properly and I was able to query the database but something has recently changed I believe, as this command doesn't work anymore. I have updated my packages and R... Any clues how can I still query

biomaRt biomaRt

updated 14.0 years ago • Adrián Cortés

I recently discovered that the application of (at least) \`norm2Filter()\` is not consistent when replicated.  I've pasted an...I recently discovered that the application of (at least) \`norm2Filter()\` is not consistent when replicated.  I've pasted an example...just a few events.  In my much larger experimental datasets, however, the number of events changes by the hu…

flowcore gate subsetting filter

updated 10.3 years ago • peterfoster

the analyses with no replicates, those with replicates work OK. Simon Anders has apparently been changing some stuff recently in his functions, so hopefully he can explain us, unless we missed an important update... switching

DESeq DESeq

updated 13.9 years ago • Michal Okoniewski

for ‘restrSiteUtils’: object ‘ifelse’ is not exported by 'namespace:IRanges'</pre> I have just recently updated R and all Bioconductor packages that I use. Is IRanges package changed somehow so exporting ifelse doesn

iranges ifelse package namespace export

updated 8.0 years ago • dalibor.miklik

array results). > >The obvious analysis problems with a focused array where most genes are >changing are: > >1. LOESS normalization assumes most genes are not changing. If most of >the genes are expected to change...there is no basis to recenter the data >around zero. The response from the lab was that they would be willing to >include 100…

Normalization limma Normalization limma

updated 20.5 years ago • Naomi Altman

function maPlot de.tags. do i need assign each gene a -1,0 or 1 to represent sig down-regulated, no change or up such is the related coding: et <- exactTest(d, pair=c("c0h","t0h"), dispersion="tagwise") summary(de <- decideTestsDGE(et

ASSIGN ASSIGN

updated 12.8 years ago • wang peter

zero normalized counts in 7 out of 8 replicates (the last one had 1 count or 1.6 counts). The fold change for comparison for such two genes was -13.4 and 2.47. Since the 'condition' has more than 3 levels I set the betaPrior to...branch of DESeq2 (v1.3), we have implemented a solution that > allows using a prior on log fold changes for factors with 3 or more levels > results. Then D…

Regression DESeq DESeq2 Regression DESeq DESeq2

updated 11.9 years ago • Noa Henig

<div class="preformatted">Dear Prof Gordon, dear Bioconductor members, I have performed gene expression analysis using Limma (Illumina human ref8) comparing two types of cells (referred below as cond1 and cond2). Based on detection call, I filtered out transcripts which are absent in both types of cells. Transcripts which were expressed only in one cell type were included in the analysis. …

limma limma

updated 14.8 years ago • Seraya Maouche

is my code: `` prol.10 = dba.count(prol, summits=250) `` <code>contrast.10 = dba.contrast(prol.10, categories=DBA_CONDITION)<br/> de.10 = dba.analyze(contrast.10)</code> <code>reads.10 = dba.count(prol.10, peaks=NULL, score=DBA_SCORE_READS...DBA_DATA_FRAME)</code> `` counts.10 = bindingMatrix.10[,4:ncol(bindingMatrix.10)] `` Should I change the summits option? …

diffbind merging_peaks

updated 8.9 years ago • veronique.storme

so basically at time 0 something was added to the cells and we want to know how expression changed along time). There are no replicates. Not having replicates seems to cause quite a lot of problems. I assume I'm just not...and that doesn't seem to work. I would like to consider genes that show a minimum of two-fold change in expression. So (I think - again, I'm a complete newbie) I need to comp…

limma limma

updated 13.5 years ago • Guest User

package](https://bioconductor.org/packages/devel/bioc/html/MesKit.html). We made some changes on the MesKit package few days ago and pushed to both the github and Biocondutor repo. However, no changes were found

MesKit

updated 4.8 years ago • wangx555

pre_dds$ids, renameCols = F) Then if you do `assay(pre_dds_collaps)`, the order of columns is changed from the original. Do I do anything wrong? Disclaimer: cross-posted in Biostars https://www.biostars.org/p/390887

deseq2 collapseReplicates

updated 6.5 years ago • gtechbio

types: Feature names: PD1 BCL6 BATF ... Feature classes: Feature categories: OK Sample names: 1P3SB 1CPASB 1P3SB ... covariatesm3<- pData(raw.D1filt) designm3 <- (model.matrix(~0 +DAdj:Ant, covariatesm3...only have these number values for the gene names. Am I doing something wrong? I know that I can change the feature names in t…

limma htqpcr

updated 10.4 years ago • julio.c.silver

EQTL green trans-EQTL purple</pre> I can create my link between 2 features like a new feature and change this color and size, but maybe it is better way to do that! How to change the color of link  between 2 features (for example...between SNP and exon) depending on their type (fro example cis-eQTL or trans-eQTL)? how to change the size of features as you did for 5UTR from Ensem…

annotationTrack Gviz

updated 10.4 years ago • Tiphaine Martin

<div class="preformatted">Thanks, Herve, I updated R , BioConductor and Rgraphviz to the latest versions. I still can't customize the edge attributes as I mentioned earlier. Any ideas? Weijun And this is my current session information. > sessionInfo() R version 2.6.0 (2007-10-03) powerpc-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils …

Biobase geneplotter Rgraphviz Biobase geneplotter Rgraphviz

updated 18.2 years ago • Luo Weijun

for each passage number). In theory (literature-based), all substances (A, B, and C) are in the same category of drugs (to treat the same disease), and A and B are the same drugs, but B is slightly modified, and C is the positive control...in a heatmap (a further subcategory of custom genes that I will provide the GeneIDs of the categories- total three categories-), volcano plot and 2) the enric…

DESeq2 passagenumber

updated 3.3 years ago • swn281

<div class="preformatted">Hello, I just made my first experiences with affylmGUI and am very excited about it. Many thanks for this! Some questions/comments rather important to me: * With three different targets, say A (complete vaccine),B (only the adjuvant), C (untreated) I am only...first experiences with affylmGUI and am very excited about it. Many thanks for this! Some questions/…

gcrma GeneSpring affylmGUI gcrma GeneSpring affylmGUI

updated 20.9 years ago • SteffenMöller

respect to this will only improve the quality of the coming release! If you have any questions or comments about this request, or if you have suggestions/changes/additions that we could or should add, please contact me (mailto

Cancer PROcess Cancer PROcess

updated 22.2 years ago • A.J. Rossini

<div class="preformatted">Hi All, Using goSeq to analyze two gene lists - up regulated and down regulated genes generated with edgeR, the up regulated list seems good, but there is an error with down regulated list. Couldn't figure out what's wrong with it. Please refer to the command line and output below. Thanks very for me for help. Steve # up list > lateTrans524up.pwf <…

GO edgeR goseq GO edgeR goseq

updated 14.2 years ago • steve Shen

out some analysis, but need help:- I have samples from two time points. The samples belong to two categories: Treatment and Placebo as follows: 005v1 Placebo 005v4 Placebo 008v1 Treatment 008v4 Treatment The ID number...would be difference in placebo and treatment sample. Now, if the question is to identify the changes caused due to the treatment, how should I define the desig…

edger

updated 7.0 years ago • candida.vaz

Hi, I have ran DESeq2 to get log2 fold changes of hypertrophy samples relative to control. (Added my code below). I think I am setting my contrast correct of Hypertrophy...vs. control correctly while getting results. My log2 fold change results are mostly in concordance with what I observe in normalized counts. Meaning, for a gene, if the control samples...have a lower mean than the hypertrophy …

DESeq2

updated 18 months ago • sropri

<div class="preformatted">Hi, There's some problem with the default value for affybatch objects (if this is the correct description) that's appeared in affy 1.12.0, which also can be seen in the affy vignette. Previously, when I typed in the name of an affybatch object at the command line, I'd get the same output as if I had put 'show(abatch)': > raw AffyBatch object size of array…

GO Survival cdf Biobase annotate genefilter multtest reposTools affy affydata graph GO

updated 19.2 years ago • Jenny Drnevich

9] "resval_9_vs_1" "resval_10_vs_1" Which indicates to me that DESeq is seeing these numbers as categories. I want to see what genes are being differentially expressed for each restoration value rank, not compare the...categories in this predetermined manner. Please let me know if I'm thinking about this in the wrong way or how to proceed with

DESeq2

updated 12 months ago • natalievillafranca

plot using circos plot. I thought of doing like sorting the value range 0.2-0.4 as hypomethylation category and range 0.7-1.0 as hypermethylation category. However, with this approach the plot again looks cluttered. Another

Circlize

updated 5.9 years ago • sinha.puja

with a gene list using GOstats. Then when I try to retrieve all genes belonging to a significant GO category I get zero genes ! I use this code: library(biomaRt) mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") temp &lt...length(temp$entrezgene) should not be zero!? This happens for multiple of my top 105 GO (BP, CC, MF) categories. Thanks for any hint ... Ina </div

GO GOstats Category GO GOstats Category

updated 14.1 years ago • Ina Hoeschele

SRX062801 SRR205889 BTW, "SRA049463" is in 'unpublished' status. Thanks for your message. Your comments will be highly appreciated. Jack --------------------------------------------------------------------- Hi, Firstly thanks to the creators of this very useful package. I've come across SRA...submission dates are often relatively old (SRA036600 was 2011-05-13) and there's metadata from mor…

SRAdb SRAdb

updated 13.6 years ago • Jack Zhu

<div class="preformatted">Hi, I am a grad student at Institute of Bioinformatics, University of Georgia, USA. I have been trying to use the bioconductor package goseq for go- term/pathway enrichment of my expression data. Since my organism of interest isn't included in the goseq database, I am manually entering the data for gene lengths and categories following the directions in the vignet…

Organism goseq Organism goseq

updated 15.4 years ago • Joydeep Mitra

the code thusly (in this case to include branches A, B, and C: <pre> meshdata("MeSH.Hsa.eg.db", category=<strong>c('A', 'B', 'C')</strong>, computeIC=FALSE, database="gendoo") </pre> However, when I run this, it just seems to hang forever and...R session without it completing. The documentation for the meshdata function includes the info that "category" argument is des…

meshes semantic similarity

updated 6.6 years ago • lisa.federer

<div class="preformatted">I am not sure I totally understand how things work. We were recently given some .gpr files that were 32 blocks each 23x24. The GAL file stated that the array was 32 x 22 x 24, and gave gene names...div class="preformatted">I am not sure I totally understand how things work. We were recently given some .gpr files that were 32 blocks each 23x24. The GAL file s…

Annotation Annotation

updated 22.3 years ago • Naomi Altman

<div class="preformatted">Hi Manasa, The bug in CustomEndNodeList should be fixed in the new release version of goTools. There was a NA value in the list at rank=2 which caused the error, the new version will remove NAs automatically. For the 3 top nodes: these nodes are included by default to ensure that the loop in the function will stop if you input some GO ids that are not children of…

Microarray GO graph goTools Category oligo Microarray GO graph goTools Category oligo

updated 18.7 years ago • Paquet, Agnes

DESeq2 to analyze differential gene expression between two groups. As I understand, the log fold changes for genes with low counts (low mean expression) should be shrunken toward zero, but in the MA-plot (see below), they're shrunken

deseq2 rnaseq

updated 9.1 years ago • lostisle

package. I have been relying on it for a while with any analysis requiring mixed model. Recently I realized that my previous results done a year ago are dramatically different with updated version. I had the exact...peaks had FDR<0.05 using version 1.28.5 while version >=1.33.11 had 0. I'm wondering if the changes in scaled weights that lead to this, and if so, what kind of situa…

variancePartition

updated 20 months ago • Le

studies from different labs and times. While we have a (functional) pipeline setup for this, I recently saw [a post][1] which mentioned using voomLmFit to counter the issues which might stem from having excess zeroes in...want to perform a group-wise comparison (with the original groups from each study), contrasting the changes between conditions. We have no repeats of condition comparisons acro…

limma voom RNASeq edgeR Microarray

updated 14 months ago • Adam Marstrand