Bioconductor Forum

new Ensembl marts for release 112 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart112 <- useEnsembl(biomart="ensembl") PS: If you want to force one previous

ensembldb biomaRt ensemblrelease

updated 20 months ago • Aleena

new Ensembl marts for release 108 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart108 <- useEnsembl(biomart=“ensembl") PS: if you want force one previous

biomaRt ensembldb ensembl

updated 3.2 years ago • Louisse

new Ensembl marts for release 107 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart107 <- useEnsembl(biomart=“ensembl") PS: if you want force one previous

ensembldb

updated 3.5 years ago • Aleena

new Ensembl marts for release 106 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart106 <- useEnsembl(biomart=“ensembl") PS: if you want force one previous

ensembl biomaRt ensembldb

updated 3.7 years ago • Benjamin

new Ensembl marts for release 105 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart105 <- useEnsembl(biomart=“ensembl") PS: if you want force one previous

ensembl biomaRt ensembldb

updated 4.1 years ago • mchakiachvili

new Ensembl marts for release 109 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart109 <- useEnsembl(biomart=“ensembl") PS: if you want force one previous

ensembldb

updated 2.9 years ago • Aleena

Hello,  I was wondering if there has been any recent change in the makeVennDiagram function of ChIPpeakAnno? I have made some venn diagrams with me BED files a couple of

chippeakanno venn diagram

updated 10.2 years ago • R.A. Tomaz

new Ensembl marts for release 104 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart104 <- useEnsembl(biomart=“ensembl") PS: if you want force one previous

ensembldb biomaRt

updated 4.7 years ago • mchakiachvili

marts for release 97 are now live on [www.ensembl.org][1]. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart97 <- useEnsembl(biomart=“ensembl") Please note that a few attributes

biomart ensembl e97 News

updated 6.5 years ago • James Allen

I recently using the same data set containing three groups undergoing static and time course analysis respectively, and...I recently using the same data set containing three groups undergoing static and time course analysis respectively, and the...1.1.291. I don't know the reason, and I would like to know if the core algorithm of the odp has been changed a lot. Thanks

edge

updated 6.6 years ago • xgt1986627

<div class="preformatted"> >From: "Law, Annie" <annie.law@nrc-cnrc.gc.ca> >To: "'jzhang@jimmy.harvard.edu'" <jzhang@jimmy.harvard.edu> >Cc: "'bioconductor@stat.math.ethz.ch'" <bioconductor@stat.math.ethz.ch> >Subject: Annotate clones Bioconductor beginner >Date: Mon, 1 Dec 2003 09:18:14 -0500 >MIME-Version: 1.0 > >Hi …

Microarray Annotation GUI annotate widgetTools AnnBuilder Microarray Annotation GUI

updated 22.1 years ago • John Zhang

Hello, I am fairly new to R and to Bioconductor and have been running some code (previously written by another member of our cohort) to analyze our mass spec data. I've run into a couple of issues which I now can't seem to fix. 1) Our peak picking code loops through large numbers of files, nearly 1500 in this most recent project, so we often run into an issue of running out of memory. For i…

software error mzR xcms

updated 6.8 years ago • abrsoule

Hello, I just want to clarify this questions: What relationship exists between the Fold Change and SLR? How can I express the SLR change with respect to the Fold? Thanks for the help!!! Laura -- output of sessionInfo(): . -- Sent

updated 13.9 years ago • Guest User

in my R-studio. My R-studio is updated (R version 3.3.1), I am using the newest version. When I type "source("https://bioconductor.org/biocLite.R")" in the console and hit enter, I get following message: "Bioconductor version 3.4...1.24.0), ?biocLite for help A new version of Bioconductor is available after installing the most recent   version of R; see http://bioconductor.org/ins…

bioconductor rstudio

updated 8.5 years ago • yog312

Hi  I am currently working on some metagenome data and I'd like to use DESeq2 tool to find the genes that are differentially abundant in different treatment over time. Due to the type of the study, I need to normalize the count data (genes abundance) per 16S rRNA copy number which changes the distribution and nature of data from count to decimal. I know that DESeq2 works on the…

deseq2 metagenomics

updated 8.4 years ago • ghanbari.msc

to simulate single-cell data, generating different populations. I am wondering if, and how, I can change values of the Differential expression paramters (% of differential expressed genes and the difference in expression...We have Diff expr: [Probability] [Down Prob] [Location] [Scale] But I do not know how to change them. THank you for your help in advance! J

splatter

updated 6.2 years ago • jp3770

<div class="preformatted">Hello, Within my lab weâve recently started trying to incorporate different CNV detection programs into our pipeline and found the intansv (http://www.bioconductor.org...div class="preformatted">Hello, Within my lab weâve recently started trying to incorporate different CNV detection programs into our pipeline and found the intansv (http...IMPORT GFF FILE …

annotate annotate

updated 9.6 years ago • Phil Ross

a matrix representing m hybridizations and sort it to extract the 2000 genes with the maximal fold change as a preliminary step of a further analysis. Is it possible to use the geneFilter to extract a fixed number of the "top

updated 21.5 years ago • peter robinson

div class="preformatted">Hi to everybody, I have started recently to analyse Illumina Bead Chip data. I started without any kind of problem and I was glad with the results until I saw...that comment from the beadarray library authors: "iScan come in a different format,.... there are two images of each array section (along

GLAD beadarray GLAD beadarray

updated 12.4 years ago • Nogales Vilardell

about the argument of tssRegion in peak annotation function of ChIPseeker. It seems that there is no change of the annotation output when I changed the tssRegion setting, from tssRegion=c(-3000, 3000) to tssRegion=c(-2000, 0). I am working...of this argument here? And, does anyone know how the promoter was defined in genomic annotation categories (promoter, 5/3 UTR, exon, intron, downstream, int…

chipseeker annotation chipseq

updated 8.2 years ago • lifeng.liu.biology

new Ensembl marts for release 115 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data as follows ``` ensemblmart115 <- useEnsembl(biomart="ensembl") ``` PS - if you want force

ensembl ensembldb biomaRt

updated 3 months ago • Ensembl_Jorge

new Ensembl marts for release 113 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data as follows ``` ensemblmart113 <- useEnsembl(biomart="ensembl") ``` PS - if you want force

ensembl ensembldb mart biomaRt

updated 14 months ago • Ensembl_Jorge

B” was given. *   I would like to find a differential expression for the following: \[fold change of  ” after treatment A” vs ”before treatment A”\], __compared to__ \[fold change of ”after treatment B” vs ” before treatment...the section “Multi-factor designs”or probably under ”Interactions” in the following great, just recently updated, vignette: https://bioconductor.org/p…

Deseq deseq2 differential gene expression rnaseq statistical test

updated 7.9 years ago • Marina

comparing normal and tumor type I (AR+), and how pairing and batch effect should be addressed? Any comments or suggestions would be very appreciated. Thank you very much in advance. Thanks, Xiayu -----Original Message----- From: bioconductor...have AR information. I am thinking to pool type and AR together into 1 column called type_AR with 3 categories: tumorNeg, tumorPos, and normal. I will us…

Normalization limma Normalization limma

updated 11.5 years ago • Rao,Xiayu

div class="preformatted"> FYI, The change log appears to be blank. http://www.bioconductor.org/changelog.html Thanks, -Steve This e-mail, including any attachments

updated 21.4 years ago • Roels, Steven

fit2 <- contrasts.fit(fit,contrast.matrix) fit2 <- ebayes(fit2) I am ineterested in log fold change between the contrast samples, but the as I see it is not there my question is how can i get the log fold change between the

updated 17.3 years ago • hemant ritturaj

R using the sequence ./configure && make && make install i built R-2.3.0 from the source, but when I try: R CMD build Biobase/ from my svn dir, this is what i get: ** arch - Frameworks /Library/Frameworks/R.framework

updated 19.8 years ago • Benilton Carvalho

Hello all, I'm analyzing a set of data that turns out to be a little unusual, but related to the recent discussions on what to do if you have a large (>40%) proportion of genes changing . I'd like some advice on my approach, particularly...other normalization method) assumes that only a small proportion of genes (~20% - 40% at most) are changing. So I ask the researcher if she would expe…

Normalization probe limma gcrma Normalization probe limma gcrma

updated 20.0 years ago • Jenny Drnevich

Warning in install.packages : package ‘DESeq2’ is not available (for R version 3.3.3) > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help A new version...of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install > ?biocLite > source("https://biocondu…

deseq2 R 3.3.3

updated 7.5 years ago • valentina.losardo

Hi, When using flowAI (1.17.1) the output changes the $GUID. With a flowFrame the $GUID changes to "V1" With a flowSet the $GUID stays the same but the $ORIGINALGUID changes...Hi, When using flowAI (1.17.1) the output changes the $GUID. With a flowFrame the $GUID changes to "V1" With a flowSet the $GUID stays the same but the $ORIGINALGUID changes to "Vx" where x is the index of the fil…

flowAI software error

updated 5.7 years ago • christopher.hall

Has anyone run into issues recently with sumitting biomaRt queries?  I am submitting a list of bacterial gene accessions to uniprot dataset and

biomart biomaRt R rstudio

updated 10.6 years ago • nickp60

list subscription request doesn't seem to have been processed yet.) Hi All, Couple of web site comments: 1) The current layout of the bioconductor.org doesn't provide much guidance to getting started with the bioconductor...Bundle' as well as adding another column to the individual package listing giving the package 'category'. More complains, suggestions, complements, etc as I get (try to) t…

Biobase edd ROC Biobase edd ROC

updated 23.6 years ago • Warnes, Gregory R

div class="preformatted">Hi, My question is about very small fold change from RMA treated data. What I did is to normalize affy chips with RMA, transform to linear values then import to GeneSpring...and gave me a list of 300 gens. What makes me confused is that 50% of these genes have fold changes less than 1.2, only 10% genes have higher than 1.5 fold change. Is this normal? I also did th…

affy GeneSpring affy GeneSpring

updated 22.2 years ago • Dapeng Cui

<div class="preformatted">Dear BioC list members, I have a few questions regarding the parameters and the output of the hclust function. I have a set of five profiles comprised of measurements of five variables (V1 to V5) in 4 different conditions (c1 to c4). You could think about these as log fold-changes for five related genes across four conditions where the values where multiplied by…

Clustering bioDist Clustering bioDist

updated 16.3 years ago • Dana Sevak

Hi I want to know what argument should be used for changing the row height in ComplexHeatmap? Thanks in advance

complexheatmap

updated 8.4 years ago • johnnytam100

How to change the size of labels in heatplot function ? I want to resize the labels in heatplot and dotplo function. Thank you

software error go dose heatplot gseGo

updated 6.9 years ago • aboumarshal

span style="line-height:1.6">How do they estimate a fold change in the following situation (normalized counts already:</span> treated1 treated2 untreated1 untreated2 10   &nbsp

deseq2

updated 10.2 years ago • tonja.r

gt;> Subject: Re: [BioC] KNN, SVM, and randomForest - How to predict >> testwithout known categories >> >> >> If algorithm 1 predicts "Yes", "Yes", "No", "No" for 4 samples and >> algorithm 2 predicts "Yes", "No", "Yes", "No", how...gt; Subject: RE: [BioC] KNN, SVM,and randomForest - How to predict samples >&g…

Microarray Clustering Category Microarray Clustering Category

updated 21.5 years ago • Kasper Daniel Hansen

Dear Mike, I was wondering about two scenarios of differential gene expression testing within DESeq2 framework. There are several components to consider -- condition (categorical; placebo or drug), survival time (continuous variable), other covariates that I want to control for (mostly categorial). 1. How would you implement design for the following question: expression of which gene is correla…

deseq2

updated 9.1 years ago • dsqquest

gene lists... on account of they didn't work so well (less correlated than just using means/fold changes). and i think this comment is ....a warning sign, too...not for you, but for all of us in the community. Estimating single gene variances

updated 22.1 years ago • Chad Shaw

Hi, I am not quite clear about the normalization in edgeR. I am not seeing any change in the actual read counts. They are same numbers except filtered for >10 reads, library size is reduced and norm.factor...is 1. Could you please comments on this? Codes: x<-read.delim("counts.txt",header=T,sep="\\t") y<-DGEList(counts=x\[,2:151\]) y <- calcNormFactors(y) s…

edger rnaseq bioconductor

updated 9.9 years ago • myprogramming2016

Rory and Bioconductors, I was using successfully Diff Bind last year, and I was picking up were I left but things are not going smoothly. The loading of the samples seem to be ok: ############# library(DiffBind) H3K4m3 = dba(sampleSheet="samplesheet_all.csv...correlations set to zero. I have no idea why this is happening. I wonder if there is something that changed in the most recent version o…

GO BSgenome BSgenome GO BSgenome BSgenome

updated 12.9 years ago • António Miguel de Jesus Domingues

following columns: ...., Conc, Conc_x,Conc_y, Fold, p-valule, FDR When I plot both the fold changes (log2FoldChange vs Fold) in a scatterplot it does not appear that these are calculated equally. The RNA DESEQ fold...changes appear to be evenly disributed over a range (-4 to -4), with alot of genes showing no major changes. The diffbind DESEQ2 analysis...however yield a strange scatterplot …

DiffBind ChIPSeqData DESeq2

updated 20 months ago • marcusn

for release 111 are now live on www.ensembl.org. If you are using the R package biomaRt, you can change your host to access our most recent data as follows: ``` ensemblmart111 <- useEnsembl(biomart="ensembl") ``` PS: if you want force

Ensembl biomaRt

updated 24 months ago • Benjamin

for release 110 are now live on www.ensembl.org. If you are using the R package biomaRt, you can change your host to access our most recent data as follows: ``` ensemblmart110 <- useEnsembl(biomart="ensembl") ``` PS: if you want force

ensembldb biomaRt

updated 2.5 years ago • Benjamin

div class="preformatted">Dear All, Recently, I found the mouse gene annotation in biomart had been changed to the version GRCm38 (mm10). However, I want to use mm9

Annotation biomaRt Annotation biomaRt

updated 13.4 years ago • lemon tree

Hi, I found cummeRbund didn't work recently. Then I found the mail: https://stat.ethz.ch/pipermail/bioc-devel/2017-June/011131.html talking about the version...changes of RSQLite to 2.0 which makes cummeRbund error. So I modify cummeRbund v2.20.0 to fit RSQLite 2.0. The code is at: https

cummerbund

updated 8.1 years ago • C.K. Shiau

<div class="preformatted">Is there a generic way to learn what is changed or new in a "released" package since its release? For instance, IRanges was released as 1.16.0 but is now at 1.16.4. I'd like...div class="preformatted">Is there a generic way to learn what is changed or new in a "released" package since its release? For instance, IRanges was released as 1.16.0 but is now at 1.1…

IRanges IRanges

updated 13.2 years ago • Malcolm Cook

about sam.plot2 Hello Mr. Holger, I have been able to use your siggenes package successfully but recently got an error about pos.stats when I tried to make a sam plot for a particular dataset. dd is a matrix of 21987 x 44, 5 groups...pos.stats must be either 0 (statistics are not displayed), 1 (stats are displayed in the upper left of the plot), or 2 (lower right). I got the same message when…

siggenes siggenes

updated 19.8 years ago • He, Yiwen NIH/CIT

applying to exon counts, there is a function called [estimateExonFoldChange][1] to estimate the fold change. I was wondering if this function, if applied to a resulting DEXSeq object that was generated using transcripts instead...find the same DTUs I wanted to have some measure to see if they at least agree (on direction of the change for example). [1]: https://rdrr.io/bioc/DEXSeq/man/esti…

DEXSeq DTU salmon rnaseqDTU foldchange

updated 6.7 years ago • fiona.dick91

I'm using Windows 7 and I need to install the networkBMA package, but I keep getting this error: <pre> Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘networkBMA’ These will not be installed</pre> Anyone knows how to help me? I...the networkBMA package, but I keep getting this error: <pre> Package which is only available in sou…

networkBMA error

updated 8.4 years ago • milenamagalhaes

Hi We have currently installed the new R-2.0 and also all the packages using the command >source('/usr/local/bin/getBioC') # Here the latest version of my GetBioC is stored >getBioC("all") -- When I try to test it, and try command...tcltk' could not be loaded -------------------------------------------------------- Can anyone comment on this. Thanks Sucheta</div

updated 21.2 years ago • Sucheta Tripathy

analysis (GSVA), can I find pathways behave different between two conditions? ChatGPT4 said changes may be subtle at the gene level but more pronounced when looking at coordinated changes across sets of genes within...pathways. Gordon comments in previous post above made me rethink about my current method. I try to find if there are papers using this method

GSVA

updated 20 months ago • Chris

Hi, I am new to bioinformatics and starting to learn recently. I have a question about gene ID if someone can guide me. I want to upload the RNA Seq data to Kegg Exp to draw pathway...Hi, I am new to bioinformatics and starting to learn recently. I have a question about gene ID if someone can guide me. I want to upload the RNA Seq data to Kegg Exp to draw pathway on...about it that it is …

annotation

updated 6.3 years ago • mnazir

div class="preformatted">Hi, Dapeng, I noticed your question about very small fold change in RMA data by GeneSpring. I encountered same problem right now. I was wondering whether you found out the solution...answer. Thanks Best regards Qiang Li Hi, My question is about very small fold change from RMA treated data. What I did is to normalize affy chips with RMA, transform to linear values …

affy GeneSpring affy GeneSpring

updated 22.2 years ago • Qiang Li

version 3.2. However, no matter what I do, I always got the following error:  <pre> > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help BiocInstaller...version 3.0 is too old for R version 3.2.2; remove.packages("BiocInstaller") then source("http://bioconductor.org/biocLite.R") A new version of Biocond…

bioconductor

updated 10.1 years ago • Jeff Zheng

Dear Support I'm working for JnJ using VPCx services. Only recently I'm getting HTTP status '429 Unknown Error' trying to install Bioconductor packages. ```r > source("https://bioconductor.org...VPCx configuration or might it be possible that Bioconductor is blokking traffic from certain IP sources? Thx in advance for answering this 'strange' question. Kind Regards Yves We…

Bioconductor

updated 4.7 years ago • Yves

if i can through limma to test directly for genes differentially expressed between right\_sided and left\_sided tumors, and not just comparing the two DE resulted lists for common genuine or diffenent DE genes (which is also..._sided & DiseaseCancer:Locationright\_sided, __which represent the average log2-fold change between the left sided tumors vs their adjucent contro…

limma microarray interaction model multiple factor design makeContrasts

updated 9.9 years ago • svlachavas

1] [1]: /media/images/fb3af932-f4c3-48ed-bb0a-ab71fc06 Question 1: since the plot has log2fold-change as x-axis labeling, does it mean when saving the report with: ``` gluc.DB <- dba.report(gluc_diff) write.csv(gluc.DB, file...in the report file also log2? Question 2: although the volcano plot shows many genes with log2-fold change between -1 to 0 and 0 and 1, the report only contain…

DiffBind

updated 12 months ago • Vera

I have been working on data from the recount3 project to integrate GTEx and TCGA data and perform DEG analysis using `DESeq2`. However, I am encountering an issue where I am getting too many significant genes while using datasets with large sample size such as TCGA-COAD and colon tissue in GTEX. This phenomenon is also mentioned here (`PMID: 35199033`), which reports that 92% of total gene in…

RNA-seq DESeq2

updated 20 months ago • Reza