Bioconductor Forum

power to detect differential expression. ``` # genes object is a character vector containing the names of genes-of-interest genes[1:5] ## "PPP3CB_AS1" "IL10RB_AS1" "PPP1R26_AS1" "RRN3P2" "AC099343.3" # Subset the data frame to contain...1] Naive_CD8_T_cells Central_memory_CD8_T_cell Effector_memory_CD8_T_cells ## 30 Levels: Central_memory_CD8_T_cell Classical_monocyt…

R limma TPM rnaseq differential expression

updated 6.2 years ago • atakanekiz

<div class="preformatted">> Date: Sun, 7 Aug 2005 20:37:22 -0700 > From: davidl at unr.nevada.edu > Subject: [BioC] Limma using all probes on Affy chip > To: bioconductor at stat.math.ethz.ch > > Hello, > > I'm sorry if this question went to the wrong place, but I would be ecstatic > if someone had the answer to it. I've …

Normalization probe affy limma affyPLM Normalization probe affy limma affyPLM

updated 20.3 years ago • Gordon Smyth

features=ebg, reads=bamfiles, mode="Union", singleEnd=FALSE, ignore.strand=FALSE) Error in names(res) <- nms : 'names' attribute [2] must be the same length as the vector [1] In addition: Warning messages: 1: In serialize(data, node

GenomicAlignments

updated 6.7 years ago • mahmudornob

if this is a source package ... OK * checking package directory ... OK * checking for portable file names ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking...halted In R, the argument of a replacement function which corresponds to the right hand side must be named 'value'. * checking foreign function calls ... WAR…

updated 20.5 years ago • michael watson IAH-C

Read the file with experiment design # The file must be previously created in Excel and saved in tab delimited format # Columns name are very important as well as capital letters...Read Gal file gene list and verify if info is there with: names(RG$genes) # If answer is NULL, do the following command #################################################################### names(RG$genes) #10 #…

Microarray Normalization geneplotter graph limma Microarray Normalization geneplotter

updated 14.5 years ago • Mathieu Olivier

if (sum(!gsg$goodGenes)>0) printFlush(paste("Removing genes:", paste(names(GE.adjusted)[!gsg$goodGenes], collapse = ", "))); if (sum(!gsg$goodSamples)>0) printFlush(paste("Removing samples:", paste(rownames...par(mar = c(6, 8.5, 3, 3)); labeledHeatmap(Matrix = moduleTraitCor, xLabels = names(datTraits), yLabels = …

wgcna

updated 5.4 years ago • zen

<div class="preformatted">Hi, I am having problems with function probes2tableBM again, and I can not figure it out what is the right ann.source for hgu133a2 chips. here is the code > mart_hs=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") Checking attributes and filters ... ok > probes2tableBM(eset, probids=featureNames(eset) [1:10],filename='llll', + …

Annotation GO Survival hgu133a2 annotate genefilter affy graph gcrma matchprobes GOstats

updated 18.2 years ago • Mayte Suarez-Farinas

see below). > class( DE_gr_iii ) [1] "numeric" > class( ALL_gr_iii ) [1] "character" > names( DE_gr_iii ) <- ALL_gr_iii > DE_gr_iii[1:10] 12808 78369 71897 241568 102075 27273 0.15805260 0.75696349 -0.02208268...F, beta=NULL ) Error in spia(de = DE_gr_iii, all = ALL_gr_iii, organism = "mmu", nB = 2000, : de must be a vector of l…

Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism

updated 15.5 years ago • January Weiner

package. After all steps, approximately 3% of LRR and 2% of BAF values turned into NA. What exactly must be the interpretation for those NA values? Must I assume a lack of signal or hybridization (just noise) for NA values

gwastools lrr baf NA

updated 10.0 years ago • Vinicius Henrique da Silva

cluster_number2 - cluster_number3 -cluster_number4 -cluster_number5, levels = colnames(coef(fit))) tmp_1_vs_all <- contrasts.fit(fit, contr_1_vs_all) tmp_1_vs_all <- eBayes(tmp_1_vs_all) top.table_1_vs_all...Gene <- rownames(top.table_1_vs_all) top.table_1_vs_all <- top.table_1_vs_all[,c("Gene", names(top.table_1_vs_all)[1:6])] …

DESeq2 DifferentialExpression limma

updated 23 months ago • michelafrancesconi8

American Pharmaceutical Company Database Personal email addresses (47,000 in total) and names for top level executives American Hospital Listing more than 23k hospital administrators in over 7k hospitals [worth

Coverage Coverage

updated 17.3 years ago • pundit

0 is the control and 1 is the test contrast <- makeContrasts(smoking_primary0 - smoking_primary1, levels = design) # fit to methyaltion set fit <- lmFit(m_norm_qc, design) fit2 <- contrasts.fit(fit, contrast) fit2 <- eBayes(fit2...Add the annotations to the results ann450kSub <- ann450k[match(rownames(m_norm_qc),ann450k$Name),…

limma methylationArrayAnalysis

updated 4.7 years ago • Kesava

code (the last statement) does not work and give the error of 'Error in shell.exec(url) : file name conversion problem' #=========== browserSession()->toto ucscTrackModes(toto)->togai tracks(toto)->toto2 tracks(togai)<-sample

updated 17.1 years ago • li lilingdu

<div class="preformatted">Hi Martin (seems like you will be the one to pick this up), I found an obscure bug in ShortRead:::.ppnCount - it'll be an easy fix, I think. I hope the code below should explain all, but if not let me know. thanks, Janet library(ShortRead) sp <- SolexaPath(system.file("extdata", package = "ShortRead")) file1 <- file.path(analysisPath(sp), patter…

updated 14.1 years ago • Janet Young

communication skills and a willingness to collaborate and to teach on an undergraduate and graduate level is a must. We expect good proficiency in English, and at least basic knowledge of the German language would be a plus. Please...communication skills and a willingness to collaborate and to teach on an undergraduate and graduate level is a must. We expect good proficiency in English, and at l…

updated 12.9 years ago • Stefanie

most genes in species A have a 1:1 ortholog in species B--that I'm hoping to just use a gene-level approach. Currently, I'm analyzing the data in two ways: (1) Align reads from both species to the reference genome of species...reference genome. Discard all genes that don't have a 1:1 orthology relationship. Change the gene names in the species B raw counts files to the names of their species A o…

deseq2 rnaseq across species

updated 8.4 years ago • vtartaglio

when running celltree: <pre> Error in apply(dists[backbone, -backbone], 2, which.min) : dim(X) must have a positive length</pre> This can be fixed by adding a drop=F such that: <pre> Error in apply(dists[backbone, -backbone, drop...F], 2, which.min) : dim(X) must have a positive length</pre

cellTree

updated 8.3 years ago • wouter.saelens

div class="preformatted"> Hi all My name is Yehudit, I am from UCLA. I am new to this forum, and to microarray analysis - hope someone could help:) Goal: trying to analyze

updated 13.5 years ago • Guest User

div class="preformatted">Hello everyone, Is there an "official" and valid cdf R package for this chip type? Best, Michal Blazejczyk </div

cdf cdf

updated 18.0 years ago • Michal Blazejczyk

Iris.CEL" "Liv1.CEL" "Liv2.CEL" "Liv3.CEL" > AF_data = read.celfiles(celFiles) All the CEL files must be of the same type. Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE Then I tried reading files separately...Liv3.CEL" > AF_data = read.celfiles(celFiles,pkgname='pd.huex.1.0.st.v2') All the CEL files must be of the same type. Error: checkChipTypes(filen…

Annotation oligo Annotation oligo

updated 12.3 years ago • Bade

packages are in C:\Users\admin\AppData\Local\Temp\RtmpaGmyKA\downloaded_packages > BiocManager::valid() * sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763...Bioconductor version '3.12' * 1 packages out-of-date * 0 packages too new create a valid installation with BiocManager::install("…

rtracklayer Bioconductor

updated 4.9 years ago • svlachavas

x, row.names=colnames(filtered))) Error in data.frame(x, row.names = colnames(filtered)) : row names supplied are of the wrong length ``` Anyone could give me a hint on why this is wrong? Thanks in advance Cecilia ``` > sessionInfo

RUVSeq software error edger

updated 6.5 years ago • ce.jim.san

p/184091/).) I'm stumped. I'm trying to plot a few transcripts at the same time, given transcript names and a TxDb. These are examples of approaches I've tried: <pre> # ------------------------------------------------------------------------------ # Setup: library(TxDb.Hsapiens.UCSC.hg19.knownGene) library

gviz

updated 9.7 years ago • stianlagstad

lt;- read.delim("normalizedData.txt",sep ="\t") ######### two class unpaired comparison # y must take values 1,2 classes <- c(-1,-2,1,2) #prepere the data for the samr analysis data.x <-as.matrix(normData[,8:11]) d=list(x=data.x...attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:8] "Row" "Gene ID" "Gene Name" "Score(d)" ... $ genes.lo : chr [1:10788,…

siggenes siggenes

updated 14.8 years ago • Assa Yeroslaviz

Ct values, already averaged over the technical repeats. I also have a header indicating the gene names (so i set _header=true_). I load my text tab separated matrix with _read.delim_ and then i use _readCtData_ like this: <pre...code>Error in data.frame(sample = 1:length(samples), row.names = samples) : <br/>   row names supplied are of the wrong length</code&…

HTqPCR readCtData Heidi Dvinge

updated 9.6 years ago • virginia.claudio

<div class="preformatted"> The Department of Biostatistics at Virginia Commonwealth University is seeking applicants specializing in genomic biostatistics for a tenure track position at the level of assistant (or associate) professor. Qualifications include: Ph.D. in biostatistics, statistics, bioinformatics, or...is seeking applicants specializing in genomic biostatistics fo…

Pathways Bayesian Cancer charm Pathways Bayesian Cancer charm

updated 16.8 years ago • Kellie J. Archer, Ph.D.

Strong emphasis will be placed on the analysis, interpretation and trouble-shooting of feature-level microarray data. The successful candidate must have excellent communication skills, the ability to work as part of

Microarray Genetics Classification SANTA Microarray Genetics Classification SANTA

updated 20.7 years ago • Higgs, Debi

Error in .testForValidKeys(x, keys, keytype) :  None of the keys entered are valid keys for 'GOID'. Please use the keys method to see a listing of valid arguments. \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# It looks like the current version became

goseq

updated 10.8 years ago • Oleg Moskvin

Hello I am new to NGS analysis and please excuse if the query is too naive. I am working on small RNA seq (tRNA fragments specifically) data. I have 3 samples each for the CONTROL and the TEST and all of them have different read numbers. I have aligned them using STAR aligner and have obtained the aligned BAM files. I am processing the aligned BAM through SALMON to obtain the transcript count ma…

DifferentialExpression DESeq2

updated 23 months ago • Dinesh

Dear all, thanks a lot for supporting such nice packages. I would like to know if limma fit function could be used with smaller set of genes or other metabolites quantified by liquid chromatography. I use limma in genes lists with thousand of genes, and never used with smaller features. I wonder if the moderated t-test could be used with only hundreds of features measured in small sample sets. …

limma metabolite data moderated t-test

updated 8.4 years ago • iglezer

have some difficulties in performing the cViz command. I get an error telling me that my data object must me atomic, but is.atmoic insists that the object is indeed atmoic. Yourdata is the example data on the homepage of ChromoViz...cViz(yourdata, cytoBand9606) #Error in sort(unique.default(x), na.last = TRUE) : # `x' must be atomic is.atomic(yourdata) # [1] FALSE yourdata2<-as.matr…

ChromoViz ChromoViz

updated 20.6 years ago • Morten

cancer research across Manchester (www.mcrc.manchester.ac.uk). The ACBBG incorporates postdoc-level bioinformaticians and computational biologists who provide collaborative support for the analysis of high throughput...in a highly collaborative and interdisciplinary environment in which multiple overlapping projects must be coordinated and run to tight, but achievable, deadlines. Direct experien…

Sequencing Cancer Sequencing Cancer

updated 13.0 years ago • Crispin Miller

hi ! I have a two factor RNA seq ,each factors have multiple levels(4 developmental stages and 16 different tissues), here is a part of my data, <table border="0" cellspacing="0"> <tbody> <tr> <td>gene

R edgeR DE

updated 11.0 years ago • feicaiyi

nbsp; All - Results/CSV Sheets/Spot Lists/\*.csv \[2015-06-25 18:05:46\]\[INFO\] Processing 3rd level Spot Analysis \[2015-06-25 18:05:46\]\[INFO\] Writing:  All - Results/3rd lvl Spot Analysis/Overexpression Chromosomal Eichment.pdf...nbsp; All - Results/Summary Sheets - Groups/Group Assignment.pdf __Error in group.correlations\[, names(S)\] : subscript out of bounds__ >…

software error

updated 10.5 years ago • Alison Ziesel

stem cell research and RNA biology. Science carried out on campus is absolutely at the top level and we carry a great state-ofthe- art infrastructure and the top research programs for the different career-level of...knowledge and fluent programming skills in R/Bioconductor and at least one more scripting or high-level programming language are essential. Applicants need to be profic…

chipseq atac-seq gro-seq bsseq rnaseq Job

updated 10.1 years ago • Jaritz,Markus

1. Average main effects of Type, Shore and Sector across all the levels. 2. Interactive effect of Type:Shore, specifically: 1. Juvenile: Inshore vs Offshore 2. Sediment: Inshore vs Offshore 3...above   My experimental design formula is as follows: <pre> ~Type*Shore*Sector</pre> Base levels for all factors are: Juvenile, Inshore, Cent…

deseq2 multiple factor design interactions design and contrast matrix contrast

updated 9.6 years ago • piensaglobalmente

Hi, I am using SGSeq and have a problem with the analyzefeatures function. Below, I have provided my code and my problems. Could you please kindly guide me? ```r library(SGSeq) library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(GenomicRanges) # Define the path to your BAM files bam_path <- "the path of my bam files" (ps: I have 41 bam files) # List the BAM files in the directory b…

SGSeq

updated 20 months ago • Sara

I keep running into the following error: Error in checkSlotAssignment(object, name, value) : assignment of an object of class “matrix” is not valid for slot ‘assayData’ in an object of class “ExpressionSet”; is(value...recommendations, particularly in terms of the `` initialize `` method, did not resolve my issue, e.g. naming all arguments and writing a new `` initialize `` met…

biobase expressionset eset

updated 7.4 years ago • andrew.birnberg

<div class="preformatted">Hi Audra, Have you tried following the examples in Sections 4.1 and 4.2 of the edgeR User's Guide? However you will probably need to learn more about R itself to be comfortable, as Sam McInturf has noted in his reply. Best wishes Gordon > Date: Sat, 14 Dec 2013 18:51:08 -0800 (PST) > From: "Audra [guest]" <guest at="" bioconductor.org=""> &a…

edgeR edgeR

updated 12.0 years ago • Gordon Smyth

So the RG object wouldn't get created and nothing was loaded. I tried saving the files under new names and trying again. I checked that everything was tab-delimited text. No luck. I also tested the files by loading them using...the older version of limmaGUI (v1.0.2) and they loaded no problem. So the files themselves must be fine. It's really quite strange. Has anyone had a problem similar to t…

limma limmaGUI limma limmaGUI

updated 21.5 years ago • Elva Diaz

to re-run a couple of new comparisons using DESeq2. I have previously used this script but something must have changed or updated in the last couple months that is responsible for this. I am trying to perform differential gene...technical replicates coldata=as.data.frame(cbind(location, temp, individuals)) row.names(coldata) = names(countData) coldata # ----------Construct data object ---------…

DESeq2

updated 5.1 years ago • Amy

but the pSize and NDE are always equal for every pathway evaluated - the top 10 are listed below. Name ID pSize NDE tA pNDE pPERT 1 Cytokine-cytokine receptor int 04060 44 44 17.81364905 1 0.000005 2 Chemokine signaling...05332 12 12 17.…

Genetics Network Organism SPIA Genetics Network Organism SPIA

updated 15.3 years ago • Will Bush

lt;- readGAlignments(bv) Error in readGAlignments(bv) : Assertion on 'more.args' failed: Vector must be named > sessionInfo() R Under development (unstable) (2015-07-07 r68639) Platform: x86_64-unknown-linux-gnu (64-bit) Running

genomicalignments rsamtools

updated 10.4 years ago • Arne Muller

packages are in C:\Users\abbie\AppData\Local\Temp\Rtmpg7ESQ3\downloaded_packages > BiocManager::valid() * sessionInfo() R version 4.0.1 (2020-06-06) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041...Bioconductor version '3.11' * 2 packages out-of-date * 0 packages too new create a valid installation with BiocManager::install(c…

software error packages update

updated 5.4 years ago • bs14ab

REACTOMEID") Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments. > mapIds(reactome.db, key = "3855", keytype...REACTOMEID") Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to…

reactome.db

updated 8.8 years ago • Lluís Revilla Sancho

Dear List, could anybody help on how to insert columns in TopTable for entrez gene id, gene name and symbol when using the hugene1.0ST arrays. When using the regular 3'IVT arrays such as the hgu133plus2 I used the following

hgu133plus2 hgu133plus2

updated 15.0 years ago • Marcos Pinho

the habitats. I am interested in which OTUs co-vary with the continuous predictor in each habitat (4 levels). I tried the following model: `` ~ Habitat + continuous_predictor + Habitat:continuous_predictor `` followed by `` results...name = Habitat_1.continuous_predictor) ``. Yet as is stated in Eaxmple 3 in the ?Results documentation: "this tests if the condition

deseq2 r

updated 8.2 years ago • fabian.roger

I have gene file in this format, everything in one column (no spaces at all): SFTPB|NM_000542.1|4506904|surfactant, pulmonary-associated protein B Is there any way to convert it in this format (into four columns) except manually? SFTPB NM_000542.1 4506904 surfactant, pulmonary-associated protein B Any suggestions? Narendra Dr. Narendra Kaushik School of Bi…

convert convert

updated 20.1 years ago • Narendra Kaushik

Hi everyone,     I am using genotype.Illumina() in  R packge crlmm to deal with Illumina genotyping data (idat file). However, some errors appear as follows:     <span style="white-space:pre-wrap">cnSet <- genotype.Illumina(sampleSheet=samplesheet, </span><span style="white-space:pre-wrap">arrayNames=arrayNa…

bioconductor

updated 7.0 years ago • junyi

countOverlaps', target signature 'GAlignments#GRanges'. "Vector#GenomicRanges" would also be valid Note: method with signature 'GAlignments#Vector' chosen for function 'countOverlaps', target signature 'GAlignments...GRanges'. "Vector#GenomicRanges" would also be valid While this is apparently harmless, a couple of questions: - What is the rationale for defining countOverlaps methods

GO GO

updated 12.6 years ago • Michael Lawrence

Hi, What is the best way to use roast for platforms where there are multiple probes per gene? Is it best to choose one probe per gene or for instance, should all probes in all the genes in a given pathway be entered? Thanks, Beth -- output of sessionInfo(): R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=Englis…

probe probe

updated 11.6 years ago • Guest User

error message: > decideTestsDGE(lrtAll) Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x),  :   'data' must be of a vector type, was 'NULL' > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86

Genetics edgeR

updated 11.2 years ago • Jon Bråte

comparison? Please correct me if I am using the wrong coding. ``` type <-factor(pheno_frame$Name) design <- model.matrix(~ 0 + type, data=pheno_frame) # Filtering, normalization, and transformation keep <- rowSums(cpm(counts...Differential miRNA between Test and Con contrasts <-makeContrasts(Test_Con=typeTest-typecon,levels=design) type <- c("Test","con…

mirTarRnaSeq miRNAData

updated 2.3 years ago • nawaz.u.toyama

I used salmon to map RNA-Seq data against hg38 from UCSC. In quant.sf i have the Ref-seq transcript IDs. I now want to use tximport to aggregate to gene level. However "TxDb.Hsapiens.UCSC.hg19.knownGene" is of little use, as they neither contain RefSeq Ids nor Gene Symbols (or am i wrong here)? What i want is exactly, what Mike did with the pre-constructed table "tx2gene.csv". I assume this is h…

salmon hg38 tximport tx2gene.csv

updated 8.7 years ago • seb.boegel

other annotation. While parsing back is possible, I assume there's a way to use the original gene name in analysis.</span>   Thanks &nbsp

cummerbund

updated 10.6 years ago • daniel.antony.pass

subscript type 'list' In addition: Warning message: In brewer.pal(n = length(unique(pData(eSet)[, f])), name = row.col.palette) : minimal value for n is 3, returning requested palette with 3 different levels ``` The additional warning...data :'data.frame': 10 obs. of 1 variable: .. .. .. ..$ condition: Factor w/ 2 levels "A","C": 1 1 1 1 1 2 2 2 2 2 .. .. ..@ dimLabels …

GOexpress

updated 3.1 years ago • grolo

dataset = dataset, verbose = verbose) : The given dataset: scerevisiae_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function.</pre>   In addition, listDatasets exhibit a

biomart bioconductor

updated 8.0 years ago • Emmanuel Levy

in useDataset("hsapiens_gene_ensembl", mart) : The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function. Thanks a million Aedin > sessionInfo() R version

biomaRt biomaRt

updated 15.0 years ago • Aedin Culhane

Hello, I am having a hard time interpreting the IHW and Shrinkage method results. I have read the paper, and also vignette and other various other question threads. I understand the purpose of the methods, however, not sure how to interpret their results. I have currently run a code: dds<- DESeqDataSetFromMatrix(countData = counts_DE_subset, …

DESeq2 RNAseq

updated 19 months ago • kcarey

geom_line() # limma design design <- model.matrix(~ 0 + g) colnames(design) <- levels(g) # with blocking on subject in duplicateCorrelation(). corfit <- duplicateCorrelation(meas, design, block=subj) corfit...How do the two treatments differ in their response over time? con.1 <- makeContrasts(B1 - A1, levels=design) fitcon.1 <- contrasts.fit(fit, c…

design limma

updated 22 months ago • SamGG