Bioconductor Forum

another treatment group B (B1, B2, B3).  For the sake of example, I had simplified the group's names to letters. The code that I use for contrast is:  "comparisonmodel <- model.matrix(~0+design) > colnames (comparisonmodel...lt;- levels(design)   fit <- lmFit(NmData, comparisonmodel) \#Applying the empirical Bayes method project.fit.eBa…

limma normalization heatmap design and contrast matrix cancer

updated 7.1 years ago • andreilazar9

I wonder if anyone has come across the same problem as I am having. I am trying to map a gene name i.e HGNC symbol to its corresponding affymetrix probe using R/Bioconductor but I don't seem to be able to do it using biomaRt

probe biomaRt probe biomaRt

updated 17.0 years ago • Ruppert Valentino

offer any insights? Thanks! Hamid --Details: > cellInfoTbl <- data.frame(cellId=names(clusterIDs), Sample="blank" , Cluster=clusterIDs, group="group") > dataset_se <- load_se_from_tables(counts_matrix = normalizedPBMC...PBMC3K", num_cores = 4) Error in checkArrayNames(exprsArray, cData, fData) : `exprsArray` must be numeric > > …

software error celaref single cell RNA-seq

updated 6.6 years ago • hamid.bolouri

value where TRUE/FALSE needed a.target <- read.marrayInfo("E-MTAB-109.sdrf.txt") > Error in names(x) <- value : > 'names' attribute [30] must be the same length as the vector [7] -- Sent via the guest posting facility at bioconductor.org

limma marray ArrayExpress limma marray ArrayExpress

updated 13.7 years ago • Guest User

at the first glance, but turned out to be tricky, either because I do not have reached the necessary level of R-savvyness yet, or because I miss something obvious. Here is the problem: I want to transform a matrix of expression...hybridizations) into an aafTable (from package annaffy). The probe IDs should be taken from the row names of the matrix and the column names should be taken from the co…

probe probe

updated 18.0 years ago • Georg Otto

<div class="preformatted">Dear list, I have a question regarding to nonspecific filtering prior to limma analysis. I've searched on google, but no answer. I have a microarray experiment with three groups: group1, group2 and group3.According to limma vignette, my analysis would be like this: f<-factor(targets$Target, levels=c("group1","group2","group3") design<-model.matrix(~…

Microarray genefilter limma Microarray genefilter limma

updated 16.0 years ago • Javier Pérez Florido

Greetings,  I'm working on RNA-Seq analysis from dog (Canis Familiaris) samples and I'm using the last genome annotation data available (CanFam3.1) from NCBI (https://www.ncbi.nlm.nih.gov/genome?LinkName=assembly\_genome&from\_uid=317138).  When I use the following code: <pre> txdb <- makeTxDbFromGFF(gtffile, format = "gff3", circ_seqs = DEFAULT_CIRC_SE…

genomicfeatures txdb canis familiaris rna-seq

updated 8.7 years ago • jggomeza

Hi Can anyone please guide me on plotting a graph showing the gene names of top differentially expressed genes in edgeR ?   &nbsp

edgeR plot differential gene expression

updated 8.1 years ago • fawazfebin

I have time-course data as "Day1", "Day2"....., when I create the list for compareCluster(), I have named the order as levels(list) = c("Day1","Day2"....), and I check the compareCluster() result, CompGO@compareClusterResult$Cluster, shows

clusterProfiler

updated 8.6 years ago • joseph

nbsp;it's not a big deal, but it would be nice if it were possible. I'd like to be able to add names to my GRanges objects when I construct them, rather than adding them afterwards. It would be convenient sometimes to...library(GenomicRanges) \#\#\# constructing a GRanges object and adding names afterwards works well: myGR <- GRanges(seqnames=c("chr1","chr2"), ranges=IRanges(start=c(10…

genomicranges

updated 10.2 years ago • Janet Young

gene expression array, but if you could just point me into the direction where to find those names for whichever chip and any associated libraries or files I need. Many thanks for any clues. Julia -- output of sessionInfo

Preprocessing Preprocessing

updated 13.0 years ago • Guest User

if (length(num) < 1 | sum(is.na(num)) > 0) stop("Please check your parameter names, which must match the \n \n colnames of phenotype files.") targetsFile <- targetsFile[, num, drop = F] nchip <- ncol(expr) targetSort...targetsFile[, num, drop = F]), , drop = F] The parameters argument specifies the column names in t…

ArrayTools ArrayTools

updated 16.2 years ago • Dick Beyer

of what needs to be visualized... >> In one case, I needed to separately visualize expression levels from >> each biological replicate, but variability was such that I had >> grouped >> them together in my model...To estimate expression levels for each >> biological replicate, I recreated a targets file, separating each &gt…

Microarray Cancer limma Microarray Cancer limma

updated 17.0 years ago • Yannick Wurm

genes which are differentially expressed. My colleague (and also myself) want to know, however ,the level of gene expression between individual contrasts for each of the genes that give rise to the LogFoldChange value We...other condition included in the contrast To my understanding, AveExp gives the log2 Expression mean level of each of the gene in all the compared arrays. Is there at least …

limma gene expression differential gene expression

updated 8.0 years ago • arfranco

I'm using the gometh() function of missMethyl and am trying to pull out the names of the differentially methylated genes from the output table, which looks like this: ``` go <- missMethyl::gometh(sig.cpg...is the number of genes that are differentially methylated. How do I find out, for example, the names of the 5 differentially methylated genes for GO:0015748? Thanks, Stewart

missMethyl

updated 5.3 years ago • stewart999

<div class="preformatted">anyone? I found that the GeneSelector package has some nice stuff for leave-1- out (and more) cross validation mark On 28/09/2009, at 11:56 AM, Mark Cowley wrote: > Dear list, > Rather than reinventing the wheel, I hope someone in the community can > point me in the right direction. > > In a pilot study, we have looked at a si…

GeneSelector GeneSelector

updated 16.2 years ago • Mark Cowley

design) >colnames(design) <- c("CTR","DIS") >cont.matrix<-makeContrasts(DISvsCTR=DIS-CTR,levels=design) >fit<-contrasts.fit(fit,cont.matrix) # here I am getting the warning message: #In contrasts.fit(fit, cont.matrix...row names of contrasts don't match col names of coefficients. I guess this is because in my eset has 1st column row names. How do I acco…

updated 14.7 years ago • viritha kaza

div class="preformatted">Hello ... In the name of aligning getBioC with reposTools, the 'relLevel' argument to getBioC() has been replaced with a boolean argument 'develOK...which defaults to FALSE. Users who wish to only receive release level software can either just use the default value or specify 'develOK=FALSE' instead of 'relLevel="release"'. Users who wish...of the 'affy' target in g…

reposTools reposTools

updated 21.6 years ago • Jeff Gentry

<div class="preformatted">if you are interested in affy array probe-level data analysis you might find this workshop interesting (see below) -rafael ---------- Forwarded message ---------- Date: Mon, 12 May 2003 15:02...div class="preformatted">if you are interested in affy array probe-level data analysis you might find this workshop interesting (see below) -rafael ---------- Forward…

Microarray Normalization GO probe affy Microarray Normalization GO probe affy

updated 22.6 years ago • Rafael A. Irizarry

retVal <- retVal[retVal[[geneID]] %in% feasibleGenes, ] ## split the table into a named list of GOs return(split(retVal[[geneID]], retVal[["go_id"]])) } ``` I created a custom OrgDb (for a non-model organism) using `AnnotationForge...and found out that custom OrgDb files created using `AnnotationForge` seem to have uppercase field names like SYMBOL and ENSEMBL in the…

topGO AnnotationForge

updated 6.7 years ago • psutton

section section 9.5 about explicit factors and section 9.7 of limma vignette about pairing on multi-level experiments. But I've received comments to use this instead (which according to the biologists the results make more...I am no longer sure which method is best. TL;DR: How to take into account paired samples on multi-level data? [1]: https://support.bioconductor.org/p/125489/</na&g…

limma

updated 4.7 years ago • Lluís Revilla Sancho

0 eliminated genes) Level 15: 71 nodes to be scored (43 eliminated genes) Level 14: 117 nodes to be scored (85 eliminated genes) Level 13: 243 nodes to be...scored (197 eliminated genes) Level 12: 463 nodes to be scored (498 eliminated genes) Level 11: 802 nodes to be scored (853 eliminated genes) Level 10: 1093 nodes...to be scored (2493 eliminated genes) Level…

topGO

updated 18 months ago • adendekk

used is arabidopsis tiling array 1.0R. However, I have problems to extract probe sequence and probe names from bpmap files provided by affymetrix. I also tried to write a tpmap file. But it doesn't seems to contain the probe names

probe probe

updated 16.4 years ago • zhen tao

is the factor and "Alveolar_macrophages" "Interstitial_macrophages" "T_cells" are the factor levels. I created the DESeq object: ``` >dds <- DESeqDataSetFromMatrix(countData = only_counts, colData = sample_info, design...Cell_type) ``` and calculated the results from the comparison of one factor level again…

deseq2 results DESeqResults

updated 5.3 years ago • paula.vaccarello

<div class="preformatted">Greetings, BioConductor users. Can you share your sysadmin experience with me? I administer R on a cluster computer system on which we use R with about 250 packages from CRAN. Now users ask me to install some BioConductor packages, which I am willing to do. However, for security reasons, I am unwilling to log in as root and run your scripts. You see what I me…

limma limma

updated 13.4 years ago • Paul Johnson

div class="preformatted">Dear all, How to filter genes from the expreSet by using the probe set names (affy)? Anyone has any clue on it? Thank you! Xin LIU</div

probe probe

updated 21.3 years ago • Liu, Xin

Prepare the 'metadata' data frame ... metadata: OK Now generating chrominfo from available sequence names. No chromosome length information is available. Warning messages: 1: In as.data.frame(data, stringsAsFactors = FALSE...Exon Rankings. If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName 3: In matchCircularity(chroms, circ_s…

updated 12.0 years ago • Guest User

<div class="preformatted">Hello, I am pretty new to marray and actually having the same problem. When using read.GenePix() I get the error ""Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed" Additionally I get a warning message ": In grep(layout.id[1], y) : Inputstring 30 not valid with this locale." When using the skip optio…

marray marray

updated 16.9 years ago • Jörg

structure_transcript_stable_id Please use the function 'listAttributes' to get valid attribute names Can anybody kindly tell me what I am missing? Thanks. > sessionInfo() R version 2.9.0 (2009-04-17) x86_64

biomaRt biomaRt

updated 16.5 years ago • shirley zhang

WIMM. Applicants should have a track record in mathematics or statistics ideally at the MSc or PhD level. Further details regarding the CBRG are available at http://www.cbrg.ox.ac.uk/. For further details about the position...To apply please send a CV and covering letter giving details of three referees, one of whom must be the current or most recent employer to Carol Eaton, Weatherall Institute…

updated 15.1 years ago • Steve Taylor

1 page):** Must contain information for at least 3 references. For each reference, the following information is to be provided: Name, title...etc.). Should include the PhD advisor as one reference. If that’s not possible, a short explanation must be provided for stating the reason (retirement, inaccessibility, etc.) for the exclusion, in this document. **3) CV (4 pages maximum...Must contain a…

postdoc Computational Bioinformatics Biology Genomics

updated 2.6 years ago • yuzun

contains entries like this one: "exm-rs1003581-131_B_F_1990477648") another column which contain names (some are in this format "exm-rs1003582" and some are in this "exm-IND6-167673849"). Other columns contain chromosome, AddressID_A...GWAStools to analyze this data. GWAStools requires for the AnnotationDataset a snpID variable which must be an integer, but that does no correspond with the SNP ID…

SNPRelate SNP GWASTools Annotation GWASdata

updated 4.0 years ago • Adrián

__Error in .check\_arg\_names(width, "width", x\_names, x\_names.label) :   when 'width' has names, they must be identical to 'seqlevels(x)'__ I recently updated my OS and installed R and Bioconductor more recent versions

teqc iranges

updated 7.4 years ago • msourdeix

How may I change the row names of an assay to make it more compatible with other R analysis? ``` > class(cancerAssays) [1] "MultiAssayExperiment" > assay

MultiAssayExperiment

updated 5.1 years ago • Dario Strbenac

div class="preformatted">hello, ? my name is Eyal and i am new to R, cut and paste level. i have created a DGEList object - d?following case study 3.3.3. i ran the calcNormFactors...table. ?> library(edgeR) > library(limma) > raw.data <- read.delim("myFile.txt") > names(raw.data) ?d <- raw.data[, 2:64] ?rownames(d) <- raw.data[, 1] ? i did not g…

updated 13.2 years ago • eyal avisar

ExpressionSet object is intended to be created parsing a matrix expression data with duplicate row names: > try(myExpressionSet <- new("ExpressionSet", exprs = myexprsunique, phenoData = myphenoData, annotation = myannotation...I was wondering if there exists a way to create this ExpressionSet object although duplicate row names exist in the expression matrix data parsed? Many than…

Annotation Annotation

updated 14.2 years ago • nqueralt@clinic.ub.es

<div class="preformatted">Hi, I try to get the vector of leaf's names from object "dendrogram" generated by cut(). For example, I have a matrix mat(100*10) rownames(mat) <- 301:400 dianaGenes <- diana...div class="preformatted">Hi, I try to get the vector of leaf's names from object "dendrogram" generated by cut(). For example, I have a matrix mat(100*10) rownames(mat) &…

updated 9.7 years ago • Ren Na

div class="preformatted">An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070504/ a20e50c8/attachment.pl</div

updated 18.6 years ago • James Anderson

Hi again! When running through my analysis of bead summary data that I have created from bead level data (background corrected with normexp, and summarised standard) I produced a topTable list which contains probeIDs...Somethings not right. So the question is: should I be creating my own controlprobe file from bead level data, as I background-corrected my data in a non-standard manner? This wou…

updated 17.8 years ago • Johnstone, Alice

aln <- readAligned("data",type="SolexaExport",pattern="*.txt.gz") ## free some mem! gc() ## the names are different from what we expect (UCSC standards), as they have an additional .fa extension levels(chromosome(aln)) ## faster...have seen when you want to use biomaRt as an annotation source ## for this easyRNASeq requires the name of the organism, which circumvent the "custom" chromoso…

RNASeq Annotation Organism biomaRt easyRNASeq RNASeq Annotation Organism biomaRt

updated 13.7 years ago • delhomme@embl.de

irradiated.0.5h irradiated.0.5h irradiated.0.5h irradiated.0.5h bystander.0.5h bystander.0.5h 18 Levels: bystander.0.5h bystander.1.0h bystander.2.0h bystander.24.0h bystander.4.0h ... irradiated.6.0h batch <- factor...where batch the 4 different biological replicates </pre> <pre> > head(batch) [1] 1 2 3 4 1 2 Levels: 1 2 3 4 design <- model.matrix(~0 …

limma multiple factor design multiple time points microarray design and contrast matrix

updated 9.1 years ago • Konstantinos Yeles

<div class="preformatted"> Tentative announcement: This course will be withdrawn if there is insufficient interest Three day course on Bioconductor (intermediate level) Instructor: Vincent Carey, Ph.D. March 5,6,7, 9am - 5pm each day Inn at Longwood, Boston Massachusetts 342 Longwood Ave, Boston MA, 02115 Tuition: $600 academic, $1200 commercial Registration form: http://www.biostat.ha…

aCGH SNP Genetics Annotation GO Visualization affy limma aCGH MLInterfaces Category SNP

updated 17.9 years ago • Vincent J. Carey, Jr.

I made a ExpressionSet from a Affy U133a spreadsheet data.      > testExp      ExpressionSet (storageMode: lockedEnvironment)      assayData: __22277 __features, 43 samples      element names: exprs      protocolData: none     phenoD…

annotation microarray R

updated 7.9 years ago • genesignature

peakset! If I directly use dba.plotVenn(KRNMWnocml,KRNMWnocml$masks$consensus) >Error in names(x) <- value : 'names' attribute [4] must be the same length as the vector [3] If I check KRNMWnocml$masks$consensus >NULL If I check

DiffBind

updated 4.8 years ago • ahua217

My experimental design is as below design<- ~ genotype + time + genotype:time There are two levels in genotype and 4 levels in time. Basically I'd like to use binomLRT test to check if there is any difference in gene expression...time2.gen2 time3.gen2 time4.gen2 Now I would use the "results" function with a "contrast" or "name" argument to get results for specific comparisons. The basi…

DESeq DESeq2 DESeq DESeq2

updated 11.5 years ago • bio2001

and with different kinds of sequences (amino acid) and received the same error message -- I'm sure I must be missing something. My R output is below. Thanks so much for any help! -- output of sessionInfo(): > genes<-keggLink("ath00906...genes[1:10,2],"ntseq") > head(sequences) A DNAStringSet instance of length 6 width seq names [1] 17…

PROcess KEGGREST PROcess KEGGREST

updated 12.2 years ago • Guest User

Hi, I have a problem using the org.Sc.sgd.db package and have questions regarding the validity of the information within the package. The results seams to be inconsistent, since `YAL068C_mRNA` describes PAU8...and `YGL261C_mRNA == PAU11`. The transcripts name for PAU9 is `YBL108C-A_mRNA` and the genename is `YBL108C-A`, which is not in the database. I crossreferenced the genes using...E…

org.Sc.sgd.db AnnotationDbi

updated 5.8 years ago • felix.gm.ernst

phenotype data, i received an error message when trying rma(my data). the message says differing names of the CEL files between phenoData and protocolData. However I don't see any obvious difference in names. I pasted my flow

biobase

updated 11.1 years ago • bin.shan

Hi, I have a question on how to define contrast when the design includes 2 level factors and an interaction term. design =~genome+condition+condition:genome. The resultsNames(dds): "Intercept" &nbsp

deseq2 deseq rna-seq

updated 11.0 years ago • solgakar@bi.technion.ac.il

created an object of 3'-UTRs and can export them as gff. But I would like to also include the gene names in the gff-file. They are there in the column Name, but i don't know how to include this in the gff-file. My script: <pre> txdb = makeTxDbFromGFF...utr) export(utr, "3_UTR.gff", format = "GFF")</pre>   I would like to also have the gene names under the column Name to…

rtracklayer gff

updated 8.7 years ago • Jon Bråte

replicates. I found the guide for limma, I am just confused about how to "makeContrasts" to get all levels of main and interaction effect. If this question is redundant, please provide the link, I could not find it. Many thanks

interactions 3factors limma Microarray

updated 4.8 years ago • Dan

what exactly means annotated raw data. Is this some thing to say that a particular spot gene name is "xxx" and it has some intensity levels xxx(ch1) xxxx (ch2) etc. If this is what is annotation component then the microarray...raw data (cDNA) already has intensity levels linked to a gene and not some arbitarary code number. Could any one please post their understanding about annotated

Microarray Annotation Microarray Annotation

updated 21.4 years ago • Ranga Chari

nbsp; <pre> > mae2 A MultiAssayExperiment object of 5 listed experiments with user-defined names and respective classes. Containing an ExperimentList class object of length 5: [1] BRCA_miRNASeqGene-20160128: SummarizedExperiment

multiassayexperiment

updated 7.2 years ago • mario.zanfardino

as indicated in the below code. I'm also including traceback, sessionInfo and valid information are below. Can you advise? Thanks, Elisabetta ```r library(tidyverse) library(Seurat) library(slingshot) library...A_AAGTGAACACTTTATC A_AAGTGAACAGTGGCTC ... D_TTTGTTGTCGGCATTA ## D_TTTGTTGTCTCAATCT ## cellData names(2): reducedDim clusterLabels ## pathnames(4): Lineage1 Lineage2 Lineage3 …

slingshot plot3d.SlingshotDataSet

updated 3.5 years ago • manduchi

RNA sequencing (gene's expressions). I am wondering if there is a way to change this package name to be more proper like \`RTCGA.RNAseq\` and if that's possible, how should I do that and to whom should I write

r developers devel

updated 10.1 years ago • MarcinKosiński

<div class="preformatted">Hello, I have assembled transcripts based on unstranded RNA-seq data. It's not the ideal experimental design, of course. Is it not possible to make a TranscriptDb object from this ? makeTranscriptDbFromGFF("transcripts.gtf", format = "gtf", exonRankAttributeName = "exon_number") extracting transcript information Estimating transcript ranges. Extracting gene IDs P…

TranscriptDb TranscriptDb

updated 12.6 years ago • Dario Strbenac

toSkip, method="density")    \# I used density method to get integer copy number levels from sample plotPeaks(CN) CN <- validation(CN) seg\_list <- list(alpha=0.01, min.width=5, undo.splits="sdundo", undo.SD=2

CNAnorm DNAcopy

updated 10.0 years ago • Venu Pullabhatla

<div class="preformatted">Dear Bioc and R List Users, I am having trouble analysing illumine data generated from BeadScan. I have .idat files and JPEG images. I realise that i need bead-level summary data to be able to begin quality control followed by normalization. Is there a way i can read .idat files for expression analysis or do i need to go back to BeadScan and generate .txt files/tif…

GO GO

updated 13.7 years ago • Ekta Jain

Treatment+Time.Point) Then I turn the columns into factors dsq$Status <- factor(dsq$Status, levels = c("Control","PNS")) dsq$Treatment <- factor(dsq$Treatment, levels = c("None","Chronic Stress")) dsq$Time.Point <- factor(dsq$Time.Point...levels = c("Before","After")) I then run DESeq dsq <- DESeq(dsq) And get the names resultsNames(dsq) …

phyloseq DESeq2

updated 3.9 years ago • dschnitzler

over 1 hour to BLAST just 10 genes). Currently, the gene identifiers I am using are simply the gene names, but it shouldn't be too difficult to derive a list of corresponding alternative identifiers (assuming they are publicly

Microarray GO Organism PROcess GOstats Microarray GO Organism PROcess GOstats

updated 11.8 years ago • Guest User