Bioconductor Forum

are taken into account, which means essentially the heatmap was made by pair-wise correlation of vectors consist of 0 and 1. But in the new version (1.6.2) I found that the vectors get from peak sets contains also a number (rather...it uses the highest score). As you say, it then computes the correlation between each pair of vectors for the heatmap. Once you have run dba.count, it uses scores b…

Transcription Cancer DiffBind MMDiff Transcription Cancer DiffBind MMDiff

updated 12.4 years ago • Rory Stark

Thanks. library(marrayInput) Monkey.info <- read.Galfile(galfile="Revised sethi-sh 136prg.gal") names(Monkey.info ) Monkey.info$layout Monkey.info$gnames > # create working dataset > datadir <- getwd() > fnames <- dir...1] "Reading ....gpr" Warning messages: 1: number of rows of result is not a multiple of vector length (arg 2) in: cbind(…

updated 22.5 years ago • White, Charles E WRAIR-Wash DC

geneList<-factor(as.integer(probekeys %in% intgenes) # intgenes= my list of interesting probeIDs names(geneList)<-probekeys str(geneList) Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ... - attr(*, "names")= chr [1:33295] "7892501" "7892502" "7892503" "7892504...object ------------------------- test.stat <- new("classicCount", testStatistic = GOFisherTest, name = "Fisher t…

GO graph GO graph

updated 12.7 years ago • Guest User

seqnames ranges strand | tx_id <rle> <iranges> <rle> | <character> [1] chr1 [ 12228, 12645] + | 1,2,3 [2] chr1 [ 12698, 13402] + | 1,2,3 [3] chr1 [322229, 324287] + | 7 [4] chr1 [324346, 324438] + | 7 [5] …

GO GO

updated 12.4 years ago • Andrew Jaffe

use. ``` DataFrame with 6 rows and 6 columns fwd rev name class type <character> <character> <data.frame> <data.frame> <data.frame> 0h-rep1 /Users/matthew/mount.. /Users/matthew/mount...29 [123] memoise_2.0.1 ``` </data.frame></data.frame></data.f…

DESeq DESeq2

updated 4.1 years ago • matthew.valentine

Hi All, When I try to download GSE49656 with GEOquery, errors were always reported: such as __not all columns named in 'colClasses' exist__   When I change to server (linux), some other error reported: __Error in read.table(con, sep = "\\t", header...I try to download GSE49656 with GEOquery, errors were always reported: such as __not all columns named in 'colClasses' exist__ &nb…

GEOquery

updated 9.1 years ago • Shicheng Guo

exons, LungCancerBamFiles()) > > Yields: > > Note: method with signature 'GAlignments#Vector' chosen for function > 'countOverlaps', > target signature 'GAlignments#GRanges'. > "Vector#GenomicRanges" would also...be valid > Note: method with signature 'GAlignments#Vector' chosen for function > 'countOverlaps', > target si…

GO GO

updated 12.6 years ago • Valerie Obenchain

methyLumiM) >> Error in apply(grnData[neg.ind, ], 2, median) : >> dim(X) must have a positive length >> >> >> I've tried to make sure that 'methyLumiM' has a controlData slot by the >> following...storageMode: lockedEnvironment) >> assayData: 14 features, 24 samples >> element names: …

Annotation Normalization Cancer probe lumi Annotation Normalization Cancer probe lumi

updated 14.6 years ago • Pan Du

Hello Günter, I noticed that '`` ExpLogFoldChange ``' in the function '`` .cn.mopsCE ``' (cn.mops.R) could either be a vector or a matrix with one row as noted in the code snippet below.   <pre>     if (all(x<=minReadCount)) {         [...]      &nbs…

cn.mops

updated 9.2 years ago • Mohammad Alkhamis

Hi all, I am running WGCNA on my big gene expression data set, and running into a bunch of errors. I appreciate any help in advance that you can provide in navigating these! First, the graph generated to choose the power is wacky looking. ![here it is][1] I chose 28, as I figured this was above the threshold. But is that elbow cause for concern? Second, going forward with a power of 28, altho…

WGCNA

updated 2.1 years ago • aehall26

<div class="preformatted">Hi, I have been looking around at examples of the hyperGTest (in the GOstats, lumi, and other documentation) and feel like I have seen many slight variations on the methodology. These variations are usually found in the way the non-specific filtering is performed. I haven't come across many examples of a hyperGTest for KEGG pathways and would like to ask whether my…

Pathways lumi Pathways lumi

updated 17.3 years ago • Sebastien Gerega

the results of unit testing. I use the following in my ~/.Makefile to see these results imidiately NAME := $(shell basename $(PWD)) # Get current map name Rcheck: # Check R package of current map (cd ..; \ R CMD check $(NAME) && \ if [ -d $(NAME)/inst/unitTests...then \ cat $(NAME).Rcheck/tests/doRUnit.Rout; \ fi) Then only the followin…

graph graph

updated 19.4 years ago • Gorjanc Gregor

I type the columns in the data.frame and get a little further as(data.frame(SeqID=character(),start=integer(),end=integer()),'GRanges') Error in validObject(.Object) : invalid class "GRanges" object: NROW(strand(x)) != length...x) Almost across the line. Let's add the strand in too: > as(data.frame(SeqID=character(),start=integer(),end=integer(),strand=…

granges coercion

updated 7.9 years ago • Malcolm Cook

error: ``` The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://support.bioconductor.org ``` Here is an example...sets (returns list of two ExpressionSets) gset_ls <- getGEO("GSE4922", GSEMatrix = T, getGPL = F) names(gset_ls) [1] "GSE4922-GPL96_series_matrix.txt.gz…

biomart geo software error ensembl

updated 6.6 years ago • wes

pheno parameter contains more than 2 phenotypes, and you want to use ProbeLasso function, you MUST specify compare.group=c("A","B"). Bumphunter and DMRcate should not be influenced. [ Section 1: Check Input Pheno Start ] You pheno...No rownamematches. 'rownames' need to match IlluminaHumanMethylation450k probe names. The same error happens when arraytype="EPIC"…

ChAMP

updated 12 months ago • André

the order of the cols and rows is the same data <- data[, row.names(metadata)] # The data must be un-logged data <- round((2 ** data) -1) DESeq2::DESeqDataSetFromMatrix( data, metadata, ~ status ) |> DESeq2::DESeq() -> dsq_obj DESeq2...results(dsq_obj, name = "status_case_vs_control") -> dsq_res cat("Deseq finished running!…

DifferentialExpression DESeq2

updated 2.2 years ago • Luca

lt;- makeContrasts(-2,2-3,3-4,4-5,5-6,6,levels=design) HOWEVER, to make this work the column names of the your design matrix must start with a letter, not a number. E.g., you need "Time2", "Time3" etc instead of "2", "3" etc. > I know there

limma limma

updated 18.8 years ago • Gordon Smyth

lt;-rma(howard1.raw) I get the following errormessage: Error in hist.default(howard1.norm) : `x' must be numeric Jim MacDonald pointed out to me that a file made with the command > dat1 <- normalize.AffyBatch.quantiles...Isaac Friedman, age 14 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1732 bytes De…

Cancer Cancer

updated 21.7 years ago • Richard Friedman

<div class="preformatted"> Iam using R version 2.15 in a linux operating system. I have a matrix consisting of the gene ids and their specific signal intensity values as follows( a subset of the whole matrix) : probes GSM362180 GSM362181 GSM362188 GSM362189 GSM362192 244901 5.094871713 4.626623079 4.554272515 4.748604391 4.759221647 244902 5.194528083 4.985930299 4.…

Annotation probe Annotation probe

updated 13.2 years ago • Guest User

<div class="preformatted"> >But when I try the widget option I still get: > >> alldata <- ReadAffy(widget=TRUE) >Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class = >"tclObj") : > [tcl] ambiguous option "-col": must be -column, -columnspan, >-in, -ipadx, -ipady, -padx, -pady, -row, -rowspan, or -sticky…

Cancer tkWidgets Cancer tkWidgets

updated 22.6 years ago • John Zhang

Min. : 5.96 Min. :-6.2495 Min. :0.1065 Min. :-5.9385 Min. :2.900e-09 Class :character 1st Qu.: 61.23 1st Qu.:-1.7460 1st Qu.:0.1518 1st Qu.:-3.8379 1st Qu.:2.666e-05 Mode :character Median : 281.04 Median :-0.5681...SYMBOL Min. :2.121e-05 Length:172 1st Qu.:9.582e-03 Class :character Median :2.859e-02 Mode :character…

DESeq2 deseq txime tximeta

updated 2.7 years ago • akrunic

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 20.6 years ago • michael watson IAH-C

<div class="preformatted"> maInd2Coord cannot index a single gene, or vector of length 1. > L <- new("marrayLayout", maNgr = 4, maNgc = 4, maNsr = 22, maNsc = 24) # Index to Coord fails for vector of length 1 (scalar) > maInd2Coord(5, L) Error in "colnames<-"(`*tmp*`, value = c("Grid.R", "Grid.C", "Spot.R", : attempt to set colnames on object with less…

updated 20.7 years ago • Marcus Davy

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 5.5 years ago • zen

gt; > > makeGRangesFromRefSNPids <- function(myids) > + { > + ans_seqnames <- character(length(myids)) > + ans_seqnames[] <- "unknown" > + ans_locs <- integer(length(myids)) > + for (seqname in names(getSNPcount...gt; > > makeGRangesFromRefSNPids <- function(myids) > + { &a…

SNP Annotation Cancer SNPlocs TranscriptDb biomaRt GenomicFeatures SNP Annotation Cancer

updated 15.0 years ago • Vincent J. Carey, Jr.

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 10.1 years ago • Vinicius Henrique da Silva

hi, Does someone know how to created matrices using rsruby? I have problems trying to put 2 ruby vectors in a R matrix. I already read the links on rsruby feeds, what I needs is working examples. I want to create boxplots and...plots with matrices. I have succeeded to do it with vectors. Thanks you very much. </div

updated 16.4 years ago • D.Enrique ESCOBAR ESPINOZA

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 17.2 years ago • li lilingdu

1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'mim_morbid_description'/><Filter...name = 'hgnc_symbol' value = 'brca2,lct' /></Dataset></Query> ################# Results from serve…

biomart getbm error

updated 10.9 years ago • Tibor Fulop

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 8.4 years ago • wouter.saelens

div class="preformatted">Dear group: I have a vector of gene symbols. I want to get EntrezID for those gene symbols. I want to use hgu133plus2 as my annotation environment...how can I do it. here is my vector: msba <- c('AURKA','CCNB2','TRIP13','EZH2','TYMS') when I have probesetid it is straightforward for me. thanks for your help. srini

hgu133plus2 hgu133plus2

updated 17.8 years ago • Srinivas Iyyer

error is: "Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:519" The code i use is showed below: library(dplyr) library(Seurat) library...this row is to decide the distribution of data #look at the cell data and change the name of upstream cluster information head(pData(monocle)) names(pD…

scRNA monocle packages Tutorial

updated 6.4 years ago • 444579004

using "new" I then want to generate a dist object > dd = dist(exprs(exampleSet)) Error in vector("double", length) : cannot allocate vector of length 582309001 or > dd = dist(exampleSet) Error in vector("double", length) : cannot...allocate vector of length 582309001 It is probable I need to reduce the data set first as most genes are not differentially expressed

marray marray

updated 14.7 years ago • john herbert

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 12.4 years ago • Bade

call)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'file' must be a character string or connection # please also include the results of running the following in an R session ![this is how

DESeq2

updated 3.4 years ago • sumitra

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 6.6 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 9.8 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 14.9 years ago • Assa Yeroslaviz

Hi, I just reinstalled TxDb.Hsapiens.UCSC.hg19.knownGene and it does not function. When I load the package, the TxDb object looks fine, but applying any function to it fails.  For example genes() gives character(0) and seqlevels() gives an empty GRanges object:     <pre> > library(TxDb.Hsapiens.UCSC.hg19.knownGene) &gt...the TxDb object looks fine, …

TxDb.Hsapiens.UCSC.hg19.knownGene

updated 8.3 years ago • l.selfors

Hi,   After doing DESeq2 with RNA seq data, the output I obtain is an excel file with ensembl transcript ID, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj. I would like to know 2 things: -If you know if there is any code that I can use in order to obtain the gene name or description in the output file instead of the ensembl transcript ID -If there is any code to obtain mor…

deseq2 gene columns output

updated 10.2 years ago • amyfm

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 9.7 years ago • virginia.claudio

mtable) : unable to find an inherited method for function "GeneSetCollection", for signature "character", "character", "KEGGCollection" How can I build my Gene set object? Thanks, Javier </div

Annotation Pathways GSEABase Annotation Pathways GSEABase

updated 16.1 years ago • Javier Pérez Florido

gt; showMethods(computeExprSet) $ Function "computeExprSet": $ x = "AffyBatch", pmcorrect.method = "character", summary.method = "character" $> and afterwards I tried to retrieve the code with $> getMethod("computeExprSet", "AffyBatch

updated 20.1 years ago • Benjamin Otto

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

p-values. The normalized expression values are in the 22283-by-16 matrix expr. The 16-long dclass vector contains the classifiers [0 1 0 1 0 1 0 ...] The goal is to compute the 22283-long vector with the adjusted p-values. Does any one

updated 22.1 years ago • Kevin Dawson

<div class="preformatted">Hi Alexander, see below for some comments. I also CCed the Bioconductor list so others can benefit from it, too. -- From: Alexander Kanitz <alexander.kanitz@unibas.ch<mailto:alexander.kanitz@unibas.ch>> Date: Tuesday, March 19, 2013 6:09 PM To: NIBR <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Subject: Fragen zu G…

Gviz Gviz

updated 12.8 years ago • florian.hahne@novartis.com

<div class="preformatted">Hi, all I am trying to use goseq for RNAseq data analysis of a non-native bacteria, I fetch the genelength data and GO term data by using ensembl Perl API. Differential expression was done by DESeq2. After data run pwf of goseq, error occurred as following: ### Error in if (hi <= low) { : missing value where TRUE/FALSE needed Have any one met this befor…

RNASeq GO goseq DESeq2 RNASeq GO goseq DESeq2

updated 11.9 years ago • 刘鹏飞

<div class="preformatted">Dear list, For the GAGE analysis, i am getting an error shown below. Error in rank(cns) : unimplemented type 'NULL' in 'greater' In addition: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' I got the gene sets, expression data and reference and target files ready for it and it seems that files are...type 'NULL' in 'greater' In…

gage gage

updated 13.9 years ago • Javerjung Sandhu

I want to obtain all human homologous gene from a Ensembl.Gene.ID vector of all Mouse genes. The df i obtain is missing many entries. Also if I use gene names instead of the Ensemble ID I have the

biomart

updated 9.2 years ago • alessandro.pastore

each row is one affy probe and each column is from one array. ## the second argument ?diagno? is a vector containing 10 group names (?treated? or ?control?) for the 10 arrays and they are in the corresponding order to the 10 columns

Pathways probe affy Pathways probe affy

updated 19.3 years ago • mike Ad.

which worked well in the paper: ``` #Error in makeTxDbFromGFF(gtffile, format = "gtf", circ_seqs = character()) : could not find function "makeTxDbFromGFF" Please how do I solve it? > bamfiles <- BamFileList(filenames, yieldSize...gt; (txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs=character())) # Error in makeTxDbFromGFF(gtffile, format = "gtf", circ_seqs = char…

rnaseqGene

updated 2.5 years ago • ikpa_p123

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 21 months ago • Sara

I'm going to be using frmatools to generate experiment-specific fRMA vectors from a set of training data, and these vectors will be used to normalize that training data as well as individual samples...independently, but I wonder if it makes sense to pool them for the purpose of generating the fRMA vectors. Pooling would obviously result in one set of vectors based on a larger dataset, and therefo…

frma frmatools

updated 10.9 years ago • Ryan C. Thompson

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

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 15.4 years ago • Will Bush

I have an AAStringSet containing the name and sequences of proteins of interest. ![Image of the stringset][1] I am trying to find from this set, hom many patterns match...EDVF or EEVF. I've try to do this but only get error codes in return saying that it needs to be a vector and not an AAstringset Object. ```r pattern <- c("DDVF", "DEVF", "EDVF", "EEVF") # str_detect(string = prot…

Biostrings

updated 13 months ago • Cédric

should get 1.6.4, which is the current vesrion on the devel arm. > > > GOLocmap<-mget(names(myGOCC$intCounts),GOALLLOCUSID); > Error in mget(names(myGOCC$intCounts), GOALLLOCUSID) : > Object "GOALLLOCUSID" not found...gt; This will be fine for almost all users > > Error in match(pkgs, libPkgs) : match requires vector arguments …

GO reposTools GO reposTools

updated 21.2 years ago • rgentleman

<div class="preformatted">Hi All, Sorry to trouble everyone but I didn't get my subsetting of an RGList sorted last week. I've tried loads of different combinations of things that were suggested but not quite there yet. MY Data is an RGList object here is a bit > R[1,1] An object of class "RGList" $G C:\\Program Files\\Agilent\\GeneSpring GX\\data\\CRX\\980\\test01_25148502098…

probe probe

updated 18.2 years ago • elliot harrison

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 15.1 years ago • Marcos Pinho

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 20.2 years ago • Narendra Kaushik