Bioconductor Forum

fit2) >results <- decideTests(fit2) >vennDiagram(results[,2:3],cex=0.7) and I get as numbers: 43 (682) 58 and outside circles 712 Looking at the mail list archive I found a line of code from Gordon to extract gene...I also found from Jim this code using affycoretools functions but it doesn't give me the right numbers and I can't understand why: > alls <- affy…

limma affycoretools limma affycoretools

updated 17.1 years ago • Celine Carret

Created a new one. in: read.affybatch(filenames = filenames, phenoData = phenoData) Enter a frame number, or 0 to exit 1: affystart(filenames = NULL, groups = NULL, groupnames = NULL, plot = TRUE, pca = TRUE, squarepca = FALSE, plottype = "pdf...1]> x AffyBatch object size of arrays=834x834 features (70650 kb) cdf=Rat230_2 (31099 affyids) number of samples=13 number of genes=31099 annot…

GO cdf annotate affy limma RBGL simpleaffy GOstats Category affyQCReport affyio GO cdf

updated 19.0 years ago • Kimpel, Mark W

mzR) Warning message: In fun(libname, pkgname) : mzR has been built against a different Rcpp version (1.0.9) than is installed on your system (1.0.10). This might lead to errors when loading mzR. If you encounter such issues...https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue. sessionInfo() R version 4.2.3 (2023-03-15 ucrt) Platform: x86_64-w64-mingw32/x64 …

xcms mzR

updated 2.7 years ago • lxl13260684135

Old packages: 'stringi' Update all/some/none? [a/s/n]: a There is a binary version available but the source version is later: binary source needs_compilation stringi 1.1.2 1.1.3 TRUE Binaries will...installation of package ‘doRNG’ had non-zero exit status > biocValid() * sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-w64-mingw32/x64 …

minfi doRNG package installation error

updated 8.7 years ago • sarka.vorackova

CELdata AffyBatch object size of arrays=834x834 features (19 kb) cdf=Rat230_2 (31099 affyids) number of samples=8 number of genes=31099 annotation=rat2302 notes= features=featureNames(CELdata) >length(features) [1] 31099...array with no Entrez-id? Thanks for any help you can provide. Naomi Altman >sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bi…

biomaRt biomaRt

updated 11.8 years ago • Naomi Altman

in Philadelphia. I am trying to use cghFLasso to analyze a bunch of Affy SNP array data for identifying copy number variations. I had no problem with installing cghFLasso package on windows desketop. But I did have

SNP affy SNP affy

updated 18.1 years ago • affy snp

I want to know which methods are commonly used for RNA seq data if the goal is to identify monotonic increasing or decreasing gene expression over time or across stages using the results of differential

DifferentialExpression rnaseqGene RNASeqData

updated 23 months ago • Shaimaa Gamal

package which human genome builds it supports without reading the documentation manually? I have to identify dependencies that do not work on a particular genome build. Thank you

build genome

updated 2.8 years ago • Dmitry

Hi I am trying to retrieve from biomaRT a GRanges of only TFs with their gene identifier metadata and was not sure about how to do this, I assume its looking through the particular biotype but not sure

biomart TF biotype ensembl mus musculus

updated 7.9 years ago • rbronste

I tried to identify the clusters in the flowdata using flowpeaks. Is that possible to extract the cluster data as a separate file individually

flowpeaks

updated 8.5 years ago • shadhiksk

We want to identify genes differentially expressed between diagnosis and relapse, so I have paired data. The Cheung simulation scenario

PROPER Paired

updated 5.4 years ago • christoph8

Dear BioC, I am tring to use Limma package in order to analyze miRNA expression. I would like to identify differentially expressed miRNA; my experimental design encompasses dye swap, and different technical replicates...swap expA3 REF expB3 REF expC3 REF I how can I set the design matrix for linear model in order to identify differentially regulated genes in respect to the comaparison between A…

miRNA limma miRNA limma

updated 18.6 years ago • claudio.is@libero.it

Dear all, Our experiments is based on gene expression of a single tissue with contrasts between 3 treatments of 3 replicates. Each set of replicates was sampled from the same population and prepared and sequenced concurrently. We have performed RNASeq as follows: 1. Align reads to reference with Salmon 2. Import data to DESeq2 with tximport 3. Identify differential expression with a (v…

deseq2

updated 6.7 years ago • Jack.Hearn

of interest and use the KEGG.db data set for it. The idea is to first extract the KEGG pathway identifier from the pathway name of interest and then use the pathway identifier to get the single genes. However, it seems

KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT

updated 5.7 years ago • tobias-messmer

countBam' with columns of 'records' (total records in file), 'nucleotides' and 'mapped'. The number in 'mapped' is the number of records returned when 'isUnmappedQuery=FALSE' in the 'ScanBamParam'. and also, ## When the reads...Shilatifard Lab - Stowers Institute for Medical Research - Kansas City PS > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unkn…

updated 11.9 years ago • Malcolm Cook

Random factor) 2, 3 or 4 biological replicates, nested in each Population (Random factor) The number of replicates is not the same in each Population and Treatment because some plants didn't grow. I am mainly interested...function: Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 91, 0 Any idea of what is going on? Is it a problem with the mod…

Microarray Microarray

updated 16.6 years ago • Aurélie Bonin

expressed genes for my first comparsion. then I do: toptable1<-topTable(fit,coef=1,number=99,genelist=genelist,adjust="fdr ") this is part of the results Name M t P.Value B 6820 H25306 2.9578622 21.779101 6.712472e...called DE gene. So I am wondering how I can select genes based on a cut off p-value rather than a number that indicates how m…

updated 21.8 years ago • p hu

<div class="preformatted">Hello I have issues in getting RCytoscape to recognize edge attributes. What I am doing wrong? Thanks! -burak rlNt();runNt("send2RCy") entering RCytoscape::displayGraph sending 11 nodes sending 22 edges adding node attributes... [1] "label" [1] "moleculeType" adding edge attributes... [1] "weight" Error! RCytoscape::setEdgeAttributes, attributes not initialized.…

graph RCytoscape graph RCytoscape

updated 13.7 years ago • Burak Kutlu

20:1968757:2004285"), : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing...list. > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS locale: [1] LC_CTYPE=en_US.UTF

software error biomart

updated 9.4 years ago • daniil.sarkisyan

eset,file="geneExpData.txt", sep="\t", quote = F); When I analyze the file written, I see that the number of columns is as I expect(number samples) but there are 33,297 genes. Please help me understand a few fundamental aspects...NAs. Can you please help me understand what is happening here. -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-unknown-linux-gnu (64-bit)…

affy affy

updated 12.5 years ago • Guest User

or something more modular). I have seen in some vignettes/tutorials that they recommend reducing the number of probes per gene to one by retaining the probe with the most variation since it will be the most informative. However...how reliable is the annotation provided? Is it completely derived from the affy annotations. The number of probes where affy entrez id and the ensemblid match is approx …

Annotation GO probe affy Annotation GO probe affy

updated 17.4 years ago • Nathan Harmston

their condition and but samples were separated along PC1 by their sex (obvious because of Xist and a number of Y-linked genes). So: 1) Is it possible to incorporate the gender of the samples into the analysis now that they are known...lt;- makeContrasts(wtVmt = mu - wt, levels=design) Using this simple design I get a very small number of significant results (2). So if I wanted to incorporate ge…

mouse4302 limma mouse4302 limma

updated 12.0 years ago • Ed Mountjoy

AGIs -- normally it works fine !) H3K27me3_BP and uBP consist of Arabidopsis Genome Initiative (AGI) identifiers. The lists are too long to post, but I could send them if needed. > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown

Annotation GO ath1121501 Annotation GO ath1121501

updated 16.6 years ago • Ulrike Goebel

Hi everyone, I am using edgeR to identify differentially expressed transcripts based on a simple RNA-seq setup (tumor vs control samples). The *DGELRT* object...reads of just the average read counts used to get the logFC values? Below is a simplified version of my code: #create DGEList object CountsTableEdge <- DGEList(counts=CountsTable, genes=rownames(CountsTable), gro…

edgeR batch-effect RNA-seq read counts ngs

updated 6.9 years ago • Roman

using biocLite. I have tried to use this example: x <- org.Pf.plasmoGO # Get the ORF identifiers that are mapped to a GO ID mapped_genes <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_genes]) if(length...Sorry to sound confused. I am pretty new to R and bioconductor. -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_…

GO Plasmodium falciparum PROcess convert GO Plasmodium falciparum PROcess convert

updated 12.2 years ago • Guest User

class="preformatted">Dear Lukas and list, I'm trying to process a set of BAM files using the latest version of MEDIPS (1.10.0), but have run into problems creating MEDIPSset objects for some BAM file. The following is an example...Hsapiens", sample_name = "0139202") Reading bam alignment 0139202.fq.sam.noDUP.bam.qf.bam Total number of imported short reads: 13813686 Creating GRange Object... …

Alignment BSgenome PROcess BSgenome IRanges MEDIPS Alignment BSgenome PROcess BSgenome

updated 12.3 years ago • Jonathan Ellis

by arguments ```sce_all_data <- cbind(sce002,sce003)``` Is this because I have different cell numbers in each sce object? After QC I have 19,989 cells in one sce and 19,943 in the other. Is there a way to get around this? Thank...you for any advice you have!! > sessionInfo( ) R version 4.0.4 (2021-02-15) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.1…

sce SingleCellExperiment merge

updated 3.6 years ago • achoppe

of behavior see "#*** and comments... It will surely catch someone out, will it use a rowname or a number , the joy of variable interpolation! Do I complain too much or is this worth a fix? > n<-8963 > fit2[8963,]$genes["ID"] ID 8963...1] "106220736" > class(fit2) [1] "MArrayLM" attr(,"package") [1] "limma" > sessionInfo() R version 2.7.1 RC (200…

updated 17.5 years ago • Paul Leo

Error en lumiR(file.i, parseColumnName = FALSE, convertNuID = FALSE, QC = FALSE, : Different column numbers of exprs and se.exprs! Please check the input data format. my sessionInfo(): R version 2.14.0 (2011-10-31) Platform: i386...udc.es ---------------------------------------------------------------- [[alternative HTML version deleted]] </div

updated 13.6 years ago • Juan Fernández Tajes

contrasts.fit (fit, contrasts_matrix) fit3 <- eBayes (fit2) test_results <- topTable(fit3, number=10, adjust="BH") # Then, I was uncertain regarding how to get the output with UniGene ID. Wonder if a bit of tweaking in the function...7,9)], html = FALSE, text = TRUE, filename = "****") Many thanks, Chintanu > sessionInfo () R version 2.9.2 (2009-08-24) i386-pc-mingw32…

Annotation GO hgu133a Annotation GO hgu133a

updated 16.2 years ago • Chintanu

CRAN (extras) 7: Omegahat 8: R-Forge 9: rforge.net 10: + CRANextra Enter one or more numbers separated by spaces, or an empty line to cancel 1: 1 2</pre> As noted in the FAQ: Some CRAN packages that do not build out of...kindly provided by Brian D. Ripley. Note that this repository is a default repository for recent versions of R for Windows.   <pre> &…

repository

updated 8.9 years ago • SamGG

in checkForExperimentalReplicates(object, modelMatrix) : The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as replicates was...v1.22. Is there anyway to avoid this error? For instance, do I have to reinstall the older version of DESeq2 v1.20? Does that mean that I would have to re ru…

deseq2 replicates error DESeqDataSetFromMatrix

updated 6.7 years ago • Yonatan Amzaleg

font face="monospace">How to fix this error?</font> <font face="monospace">I have edgeR version 3.12.0 installed.</font>   &nbsp

edger rna-seq

updated 9.9 years ago • Koen Van den Berge

I keep getting this error with autoplot (or plotIdeogram) in ggbio.

Error in rep(startY, each = length(yy)) : 
  attempt to replicate an object of type 'language'

Wondering if it has to do with the ggplot2 (3.1.0) as suggested by this [issue](https://github.com/tidyverse/ggplot2/issues/2610). Following is a sample of my code:

library(ggbio)
library(biovizBase)
data(hg19Ideogra…

ggbio ggplot2

updated 7.0 years ago • t.fadason

3 samples) using bootstrap. R is running out of memory ('Error: cannot allocate vector') when the number of genes (5413) combined with the number of bootstrap iterations (B=10000) produce a large matrix. I am running R on PowerBook...read *only* the gcrma-processed dataset (nothing else) into a new R session ## to reduce the number of objects in memory: > load("esetGcrma.rda") ... >…

genefilter PROcess genefilter PROcess

updated 17.8 years ago • Timur Shtatland

I try it with real data, I get a "subscript out of bounds" error in `irwsva.build`: ? ? $ R ? ? R version 2.15.0 (2012-03-30) ? ? ? ? ? > trainData <- read.table('http://www.broadinstitute.org/~ljosa/svaproblem/trainData. txt') ? ? > trainpheno...lt;- model.matrix(~1, trainpheno) ? ? > trainSv <- sva(trainData, trainMod, trainMod0) ? ? Number of significant su…

sva sva

updated 13.4 years ago • Vebjorn Ljosa

RData objects generated in the previous step and I noticed that procodingseq reports ENST identifiers in both tx_name and pro_name fields and proteinseq reports ENSP identifiers in both tx_name and pro_name fields...package="proBAMr")) but the corresponding proteinseq and procodingseq objects report ENST identifiers in both tx_name and pro_name fields and I cannot generate the SAM file at al…

proBAMr PrepareAnnotationGENCODE Gencode annotation

updated 6.0 years ago • laura.fancello

<div class="preformatted">Hi everybody, I have to come back to the issue of replicates probes in the Agilent 4 x 44K. Reading for example the answer of Gordon Smith http://article.gmane.org/gmane.science.biology.informatics.conductor/1 3846/match=agilent+probe+replicates I completely agree with him to treat the replicated probes, doing the analysis to select the differentially expressed p…

GO GO

updated 17.8 years ago • Daniela Marconi

I'm doing this, but what if?) What I'd like to do is filter the gene list so I can cut down on the number of tests in the multiple testing routine (and hence get better numbers). * What exactly is the expression value that RMA...gt; to be expressed? > > In addition (please correct me if I'm wrong), using > only the number of expressed genes (or at least not > all of …

multtest affy multtest affy

updated 22.3 years ago • Bob

in non-model organisms? I'm working with the axolotl, and I am wondering what tools and with which identifiers people would typically work with

axolotl KEGG GOstats clusterProfiler

updated 2.4 years ago • georgii.vdovin

Hello, I have a unannotated lncRNA seq (~2K) that was identified by a study from online literature.  I want to use the RNA-seq data (e.g., TCGA) to quantify this lncRNA expression

rnaseq

updated 9.2 years ago • xiaoyonf

div class="preformatted">Dear R Experts, Is there any package for identifying peptides from MS/MS data using R. Any help or pointers in this regard is highly appreciated. Thank you in advance

updated 15.8 years ago • Kishor Tappita

<div class="preformatted">Dear List, I'm trying to find out the best procedure to treat the following "triangular" experimental plan. Three groups of samples (prepared as triplicates and run on 3+3+3=9 microarrays) are to be compared in the way where those elements/genes that are different in each of the three groups should be identified (ie, (av1 != av2) & (av1 != av3) & (…

limma limma

updated 16.2 years ago • Wolfgang RAFFELSBERGER

to use arabidopsis tiling array(1.0R) to do the > whole transcriptome mapping, especially for identifying new transcripts, > so it's kind of expression level study. I'm performing some analysis > referring to your book...be used for many things: transcript boundary > mapping, new transcript discovery, DNA copy number variation, ChIP, > genotyping, polym…

Microarray GO cdf Microarray GO cdf

updated 16.8 years ago • Wolfgang Huber

<div class="preformatted">Hi, I was trying to get significant KEGG terms for yeast. Previously, I used the "YEAST" package, but I am now shifting to the "org.Sc.sgd.db" package. A sample of the code, and the error I get is reproduced below: ------------------------------------------------ Begin code ----------------------------------------------------------------- ## TEST HYPERGTEST FOR K…

Annotation GO Yeast hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hgug4110b hgug4112a GO

updated 16.9 years ago • Paul Evans

genome="hg18") affymetrix tiling The package will be called pd.hs.prompr.v02.3.ncbiv36.affy Array identified as having 914 rows and 914 columns. Creating package in /export/share/disk501/lab0605/mrobinson/projects/ microarray...hg18") affymetrix tiling The package will be called pd.hs.prompr.v01.3.ncbiv36.nr.harvard Array identified as having 914 rows and 914 columns. Creating package in /export/…

affy affxparser affy affxparser

updated 17.4 years ago • Mark Robinson

each being a subset of the other. My original query consists of retrieve GO terms for 5032 UniProt identifiers. The full query is described below <pre> library("biomaRt") attr <- c("uniprot_swissprot", "go_id", "namespace_1003", "name_1006...damaged DNA binding ISO </pre> I am focusing in the results for 3 protein identifiers in particular <pre> id0 …

biomart

updated 8.6 years ago • Laurent Gatto

chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000001 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NONHSAT000001 // NONCODE // Non-coding transcript identified by NONCODE: Linc // chr1 // 100 // 100...0 // --- // 0 /// NONHSAT000002 // lncRNAWiki // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 0 // --- // 0 /// NON…

ClariomDHuman Annotation 3 groups

updated 6.1 years ago • jiamacro

Hello there, I am running a KEGG enrichment analysis but about 2500/14700 genes do not get converted to KEGG identifiers using keggConv. Presumably this is because they are not in the KEGG database. Should we exclude those 2500 NA genes...I am running a KEGG enrichment analysis but about 2500/14700 genes do not get converted to KEGG identifiers using keggConv. Presumably this is because t…

KEGGREST KEGG RNASeq

updated 2.1 years ago • mch

with some of the codes. For Gene Set Analysis, the user has to inputs: 1)CELL Files 2)choose identifier type 3)choose GO 4)choose the pgsea method. What I actually do is determing in the code below where to pass the identifier

microarray pgsea

updated 9.8 years ago • livdiehard

can achieve a merged MA plot from my six slides basically I'd like to be able to plot this data and identify particular spots using identify() thanks -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute

limma limma

updated 22.2 years ago • Jason Skelton

by the negative control probes on the array (Aliens and Human sequences). These would hopefully identify a set of genes that are expressed vs not-detectably-expressed in my tissues of interest. I have a loop design, and am...using limma to identify differentially expressed genes. Is it possible to use limma to also do the analysis I suggested above? I assume that

limma limma

updated 18.8 years ago • John Fowler

and different lanes We’d like to compare each data set to each other, but really the goal is to identify genes that are DE in the nCe samples compared to all others.  We’d like to control for variation due to sequencers...full=~flowcell + condition, reduced = ~ flowcell) Would this be an appropriate analysis that would identify genes DE in nCe vs others? thanks Charles

deseq2

updated 8.5 years ago • charlesh

I am currently working with Clariom D Human Microarray. After normalization of the data with RMA{oligo}, I get  138745   features which I need to annotate for the downstream analysis that includes differential expression and gene enrichment steps. I would like to assign a gene identifier to a given probeid using the select() function of {AnnotationDbi}: __>all.e…

annotation clariomdhumantranscriptcluster.db oligo

updated 8.8 years ago • yahia.adnani

lfcThreshold = 1, altHypothesis = "greaterAbs", independentFiltering = T)</pre> This allowed me to identify the DE genes between the average of the transcriptional effects of x, y, z and their simultaneous effect (xyz). Currently...transcriptional profile of simultaneous xyz overexpression. Which basically, translates to``   ``identify the coefficients for the`` results ``funct…

deseq2 contrast

updated 8.8 years ago • sebastiano.curreli

number=3412,adjust.method="BH" ,p.value=1) write.table(s24vss48,file="s24vss48.txt",sep="\t") s48vss96<-topTable(fit2,coef="s48vss96...number=3412,adjust.method="BH" ,p.value=1) write.table(s48vss96,file="s48vss96.txt",sep="\t") c0vsc24<-topTable(fit2,coef="c0vsc24...number=3412,adjust.method="BH",p .value=1) write.table(c0vsc24,file="c0vsc24.txt",sep="\t") c24vsc48<-to…

updated 16.8 years ago • Sally

gt;I would like to now also about the correlation of the replicates, so I >entered as replicate number 4 and as distance 21 (according to >"Bioinformatics+ computional statistics using R and Bioconductor" the >distance...corresponds to the number of spots that lies betweeen the >replicates). >But I get the following message: > >"Error in dim(M)&…

GUI limma microRNA GUI limma microRNA

updated 17.2 years ago • Naomi Altman

<div class="preformatted">Dear list, We are looking for a Post-doc / PhD to set up management and analysis of next generation sequencing data in our genomics team. The successful candidate will process and manage sequencing data, solicit and perform data analysis of genome sequencing experiments, implement existing analysis pipelines and associated data flows. You should have a degree in …

Sequencing Genetics Classification Cancer PROcess Sequencing Genetics Classification

updated 16.1 years ago • Reek, J.

1.4 -0.5 1.5 -0.6 1.6 -0.7 1.7 -0.8 1.8 -0.9 1.9 -1 2 This removes negative numbers? What is the reason for doing this? [[alternative HTML version deleted]] </div

updated 14.6 years ago • john herbert

filenames = celFiles) Error in validObject(.Object) : invalid class "AffyBatch" object: 1: sample numbers differ between phenoData and protocolData invalid class "AffyBatch" object: 2: sampleNames differ between phenoData...and protocolData > all(celFiles %in% list.files()) [1] TRUE > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Unite…

updated 16.1 years ago • Fraser Sim