Bioconductor Forum

Hi all, Would you please tell me how to fix the error below? Thank you so much! Update: I fixed the error. Thank you. ```r my_obj <- findmarkergene...tissue = "Blood") There are 1255 potential marker genes in CellMatch database for Human on Blood. Error in $<-.data.frame(*tmp*, "cluster", value = character(0)) : replacement has 0 rows, data has 979 sessionInfo( ) R version 4.…

scCATCH

updated 3.3 years ago • Chris

Hi all, I'm trying out a preservation analysis in WGCNA. I constructed modules from two different treatments (same genes, different...samples) and now want to compare the modules. But, I'm running into this error with R version 4.0.0. I had the same error when importing the RData of module colors from previous network analyses: ```r...hybrid", nPermutations = 20…

preservation WGCNA

updated 4.1 years ago • Sara

div class="preformatted"> Hi, I am having a problem with AnnBuilder: Error in "[.data.frame"(annotation, , 1:3) : undefined columns selected The code that generate this error is below: > myBase <- "ProbeIdToLL.txt...gt; myBaseType <- "ll" > myDir <- tempdir() > mySrcUrls <- getSrcUrl("all", "Mus musculus") > ABPkgBuilder(baseN…

GO Organism annotate AnnBuilder GO Organism annotate AnnBuilder

updated 20.0 years ago • Sylvain Pradervand

Hi I have been trying to get BeadExplorer to work with my Illumina data, but I get the following error when using either the txt or csv files: > data<-beadAnalysis() Read c:/R/Illumina/Sample_Probe_Profile.csv Error in...message: read.phenoData is deprecated, use read.AnnotatedDataFrame instead I do note that this error has been posted on here before, but I haven't seen a resoluti…

BeadExplorer BeadExplorer

updated 18.3 years ago • Johnstone, Alice

<div class="preformatted">Dear all, I would like to use affycomp for my data, but even using the example data "s_RMA.csv" I get the following error when trying to read the data: > s <- read.spikein("s_RMA.csv") Error in function (classes, fdef, mtable) : unable to find an inherited method for function "pData", for signature "phenoData" > sessionInfo...div class=…

affycomp affycomp

updated 17.1 years ago • cstrato

msg says that it couldn't load gvc.3.dylib, I guess that's because it couldn't find it. Li > HI, All, > > I'm running R 2.6 on MacOSX, I installed the "Rgraphviz" version > 1.16.0 with no trouble at all. But when I tried to load...the library I > got error message as below: > > > library(Rgraphviz) > Loading required package: graph…

updated 18.0 years ago • Li.Long@isb-sib.ch

div class="preformatted">Hello, I am having a strange error message when calling backgroundCorrect with normexp in limma: Error in if (all(abs(delta) < 0.0000000001)) break : missing...value where TRUE/FALSE needed I was able to track the error to the call to optim within normexp.fit but that is as far as I got. Unfortunately, it is particular to this array, as for...PositionY")) ar…

updated 17.4 years ago • Augusto Rendon

I received this error when running `cn.mops()`: ``` Error in if (all(segMedianT == 0)) { : missing value where TRUE/FALSE needed ``` The issue occurs when the for...segment, + minSeg=minWidth) Error in if (all(segMedianT == 0)) { : missing value where TRUE/FALSE needed ``` Thought I would let you know! Best, Henry Miller

cn.mops

updated 6.2 years ago • millerh1

to look in the rat database and get the  ENTREZID with the probes I extracted before. and this error pops `` Error in USEMethod("select_"): `` `` no application method for 'select_' applied to an object of clad "c('ChipDB', 'AnnotationDb...both R version 3.4.1 and 3.3-PreUgrade and I could only make it work once it the pre-ugrade, but the error appeared again upon using it in a functi…

bioconductor dplyr select

updated 8.2 years ago • abedini.jaleh

to investigate, everything went well. However, when the number of chromosomes increased, some error appeared (only in BiocParallel ). ```r inputExp <- ChIPQC(samples,annotation = "hg19",chromosomes=c(1,2)) ##Error: BiocParallel errors...0 remote errors, element index: ##8 unevaluated and other errors ##first remote error: ``` I have tried method like adding "BPPARAM <- S…

BiocParallel ChIPQC

updated 15 months ago • Young Boqin

Hi all, I am trying to parse through a GenBank file and I keep getting this weird error : ``` parseGenBank(file) Error in .Call2("new_XString_from_CHARACTER

genbankr parseGenBank gbk error

updated 6.6 years ago • ashley.dederich

div class="preformatted">Hi, all, The following error message was generated when I used "mva.pairs()" function to plot my data. "Error in simpleLoess(y, x, w, span

updated 20.9 years ago • Puhong Gao

<div class="preformatted">Hi All: I am trying to analyze C. elegans tiling array data using the AffyTiling library. I use the bpmap file provided by Affymetrix. The program reads CEL & bpmap files but exits with error message after traformation (see out put below). Can anybody explain how I should avoid this problem? Any help would be appreciated...div class="preformatted">Hi Al…

updated 15.1 years ago • Feseha Abebe-Akele

Hi i was trying to running example code of PureCN, but i got two error: 1. I did not find any function called "createTargetWeights" after installing PureCN. 2. While running "runAbsoluteCN...Hi i was trying to running example code of PureCN, but i got two error: 1. I did not find any function called "createTargetWeights" after installing PureCN. 2. While running "runAbsoluteCN" of...section 5…

PureCN

updated 9.3 years ago • rahulk.aiims

Dear all, I use cn.mops to call CNV in tumor-only samples, My data is Targeted DNA sequencing data. Preparations: I have prepared sorted...X <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr,mode="unpaired",) `` and ran into this error infomation: ![](file:///C:/Users/%E9%87%91%E9%91%AB%E6%B5%A9/AppData/Local/YNote/data/jinxinhao1988@163.com/3ef556b4378b4dbabbd76987c2f7c…

targeted sequencing cn.mops

updated 8.0 years ago • jinxinhao1988

Hi all, I used a different reference genome to align instead of GRCh38 and got this error: result <- dba.blacklist(result) Genome...removed. result <- dba.blacklist(result, blacklist = BSgenome.Hsapiens.1000genomes.hs37d5) Error in dba.blacklist(result, blacklist = BSgenome.Hsapiens.1000genomes.hs37d5) : object 'BSgenome.Hsapiens.1000genomes.hs37d5

DiffBind

updated 2.6 years ago • Chris

filters = 'affy_ath1_121501', values = affyids, mart = ensemartplants) I get the following error: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 156 did not have 8 elements I seems that the file...coming back has a value that does not have all 8 attributes, but I don't know how I could fix that. Matthew The information in this e-mail is intended only…

updated 13.3 years ago • Matthew McCormack

March 28, 2013 2:52 PM To: Shields, Rusty (IMS) Cc: r-help at r-project.org Subject: Re: [R] Error in setMethod("combine"... was - Error when installing globaltest package On 3/28/2013 11:05 AM, Shields, Rusty (IMS) wrote: > Hi...Sent: Tuesday, March 26, 2013 12:34 PM > To: bioconductor at r-project.org > Subject: [BioC] Error when installing globaltest package > &…

Infrastructure Cancer Biobase tkWidgets globaltest BiocInstaller BiocGenerics Cancer

updated 12.8 years ago • Shields, Rusty IMS

genechip HT430PM I've installed the required libraries(affy, arrayQualityMetrics, htmg430pmcdf) and all dependecies I'm using the following code: fls <- list.files("/", ".*CEL") eset <- justRMA(filenames = fls) aBatch <- ReadAffy(filenames...fls) arrayQualityMetrics(aBatch,outdir = "report") The last commad shows the following error message: The report will be written in di…

cdf affy arrayQualityMetrics cdf affy arrayQualityMetrics

updated 16.0 years ago • Ramzi TEMANNI

pkgconfig_2.0.3 ``` Other notes: 1) I originally discovered this error using the command line interface through the featureCounts [Snakemake wrapper](https://snakemake-wrappers.readthedocs.io...That's just to say the bug is not specific to the R-interface. 2) It is an oddly infrequent error. Most instances where a set of reads is consistent with several annotated isoforms yiel…

featurecounts Rsubread

updated 24 months ago • isaac.vock

Hi all, After googling and ask chatGPT, I don't know how to fix this error. Would you please have a suggestion? Thank you so much! gene_sets_dir...c2_list <- qusage::read.gmt(c2_gmt_file) # geneSets <- getGmt(c2_gmt_file) also get the same error. GeneSets is large genesetcollection. w <- arrayWeights(numeric_matrix, design) fit <- lmFit(numeric_matrix, …

CAMERA limma

updated 20 months ago • Chris

during the Model tuning step I get the following error: In mclapply(1:nrow(ud), FUN = function(x) iClusterPlus(dt1, dt2,  :   144 function calls resulted in an error   __Also...if I simply try the __ all(rownames(hn.cn)==rownames(hn.mut)) \[1\] TRUE fit.single=iClusterPlus(dt1=hn.cn,dt2=hn.mut,type=c("gaussian","binomial"),  &nbsp...nbsp;&…

iCluster software error

updated 10.2 years ago • perdomos

Hello all, I was using limma for assessing the deferentially expressed genes in my microarray experiment. However, during the analysis...process I've encountered the following error <pre> Error in chol.default(Zinfo) : the leading minor of order 11 is not positive definite Calls: arrayWeights -> chol -&gt...chol.default Execution halted</pre> I guess this error is…

limma

updated 9.5 years ago • venu

with a specific dataset, where genes (rows) were sorted by abundance, I have observed the following error: > Error in (function (cond) : error in evaluating the argument 'args' in selecting a method for function 'do.call': BiocParallel...errors element index: 3 first error: error in evaluating the argument 'x' in selecting a method for function 't': no right-hand side...i…

DESeq2 BiocParallel

updated 4.5 years ago • Steffi Grote

div class="preformatted">Dear All, I am trying to load ShortRead package but I get the following error: library(Biostrings) library(ShortRead) Error : object...compact? is not exported by 'namespace:Biostrings' Error: loading package/namespace failed for 'ShortRead' Any suggestions? Cheers Raffaele ########################################################## sessionInfo() R version 2.13.0 (2…

ShortRead ShortRead

updated 14.7 years ago • raffaele calogero

div class="preformatted">Dear list, I am getting the error listed below when i try to run the "gage" function within GAGE package: Error in rank(cns) : unimplemented type 'NULL' in 'greater...containing 1406, 17, 10, 8, 150, 124, 91, 162, 58 and 290 genes respectively. I am able to read all the input files properly. I have done multiple GAGE analysis before but i didn't get error of this kin…

gage gage

updated 13.7 years ago • Javerjung Sandhu

div class="preformatted">Hi All I am analysing affymetrix data, and I am trying to use "limma2annaffy" function from "affycoretools" package to create html...pval = TRUE, FC = TRUE, expression = TRUE, html = TRUE, text = FALSE, save = FALSE) I get the error: "Error in round(fld, 2) : Non-numeric argument to mathematical function" In order to understand why I get this error, I have...Whe…

GO hgu133a2 GO hgu133a2

updated 14.9 years ago • mali salmon

<div class="preformatted">Hi, I am trying to use DEseq to assess differential expression between two conditions "DE" and "un". I have 7 sets of comparisons. All my RNA-seq libraries do NOT have biological replicates. conds <- c("C.14.car.un", "C.14.car.DE", "C.14.mid.un" , "C.14.mid.DE", "C.14.sal.un", "C.14.sal.DE", "C.01.car.un" , "C.01.car.DE", "C.01.mid.un", "C.01.mid.DE", "C.…

DESeq DESeq

updated 13.8 years ago • mariangela bonizzoni

like so: <pre> dds<-estimateSizeFactors(dds,type="iterate")</pre> and get the following error: <pre> Error in estimateDispersionsFit(object, fitType = fitType, quiet = quiet) : all gene-wise dispersion estimates are within...function as advised: <pre> dds <- estimateDispersionsGeneEst(dds)</pre> and get this error... <pre> Error in .…

deseq2

updated 8.6 years ago • brijon

Hi, I tried to plot the graph from `` showSigOfNodes `` but I got the following error: goNodes <- showSigOfNodes(sampleGOdata, + score(resultKS.elim), + firstSigNodes = 5, + useInfo='all') > svg(paste(comparisons...goNodes.svg")) > plot(goNodes) Error in xy.coords(x, y, xlabel, ylabel, l…

topgo svg

updated 8.3 years ago • mictadlo

Hi, I got this error while installing ReportingTools: Error in download.file(url, destfile, method, mode = "wb", ...) :   cannot download all files

reportingtools

updated 9.5 years ago • Asma rabe

<div class="preformatted">Dear All, I am trying to use Ringo for analysis of Agilent platform ChIP-chip. I get the following output/error when applying the computeRunningMedians function to my expression set (2 samples, one normal and one dye- swap): Chromosome 1 ... 170809ds ... 261108no ... Chromosome 10 ... 170809ds ... 261108no ... Chromosome 11 ... 170809ds ... Error en newExprs[…

Ringo Ringo

updated 16.4 years ago • Diego Villar

Axel Klenk for the advise to use it) first on PC and now on MAC. I realize that it is can't run at all on MAC, while on PC it does work, although not as described (or at least not all features described in the vignette are functional...package ?affyPLM? Creating a generic function for ?hist? from package ?graphics? in package ?affyPLM? Error in as.environment(pos) : no item called "newtable" o…

limma affyPLM arrayQualityMetrics limma affyPLM arrayQualityMetrics

updated 13.9 years ago • Vladimir Krasikov

div class="preformatted"> When updating to Bioconductor 2.14 I get the following error from Rgraphviz. In file included from LL_funcs.c:1:0: common.h:16:17: fatal error: gvc.h: No such file or directory compilation...terminated. make: *** [LL_funcs.o] Error 1 ERROR: compilation failed for package ???Rgraphviz??? The server runs Ubuntu 12.04 (LTS) and the necessary packages are available...2.…

graph graph

updated 11.8 years ago • Guest User

Dear Sir, i am doing work on microarray data analysis in R using Bioconductor. i have installed all the default packages and other required packages. when i used  "qc(myobject)" , i am getting the following error...message: Error in setQCEnvironment(cdfn) :   Could not find array definition file ' drosophila2cdf.qcdef '. Simpleaffy does not know

Microarray cdf Microarray cdf

updated 15.8 years ago • NUTAN CHAUHAN

div class="preformatted"> Hi all, Im very new to R and Bioconductor so please forgive my poor language! I've been trying to ma on my list of probeIDs the relative...annotation but unsuccessfully. I get this error The object "probes" is a data.frame so maybe a should change its class? How would i do that? Thanks a lot -- output of sessionInfo...symbols <- mget(probes,mouse4302SYMBOL,…

updated 13.2 years ago • Guest User

mzmin"=216.1321,"mzmax"=216.1361,"length"=20,"intensity"=1000) but I keep getting the following error...Error in validObject(.Object) : invalid class “CentWaveParam” object: 'roiList' does not provide all required fields! I don

roiList xcms centwave XIC

updated 6.5 years ago • roxana

div class="preformatted">Hi all, I've run into a problem when attempting to install the globaltest package from Bioconductor. I'm using R 2.14.0 on 64bit...Creating a generic function for âresidualsâ from package âstatsâ in package âglobaltestâ Error in setMethod("combine", signature(x = "gt.result", y = "gt.result"), : no existing definition for function âcombineâ Error : unable...to loa…

BiocInstaller BiocInstaller

updated 12.8 years ago • Shields, Rusty IMS

the Heatmap function for making a heatmap with 9000 rows. It works properly. Then I converted all the numbers to 0 and 1 and tried running the same script again. It showed only a part of heatmap. I tried reducing the number...please help. I am unable to understand what happened here or why it didn't work ? There was no error or warning message. Later I increased the memory to 20GB used t…

Complexheatmap

updated 6.9 years ago • Goku

div class="preformatted">Dear All, I have my files downloaded from Arrayexpress say (E-GEOD-6728). Because it is large in size, I donot want to download it everytime...as it is in binary format. Can anyone please help as whenver I use magetab2bioc() it gives me an error while using my local files stored? Thanks in advance. [[alternative HTML version deleted]] </div

ArrayExpress ArrayExpress

updated 14.8 years ago • pratibha mani

div class="preformatted">Hi all, When creating pwf I encounter this type of message: > pwf <- nullp(genes, "hg19", "ensGene") Loading hg19 length data... Error in

updated 12.6 years ago • Emanuela

I'm working with mouse data and I want to create a dataframe with two columns: 1) the list of all mouse GOIDs 2) all genes *in each GOID* Basically I want to do something like this: ``` library("GO.db") library("org.Mm.eg.db") go_terms_mouse

go annotation

updated 5.8 years ago • theodore.killian

div class="preformatted">Hello All, I wrote a script to analyse affymetrix data but its giving an error while using the topTable from limma: Error in array(x...x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type I checked all the steps that might be causing the error but couldn't find out. So, I trimmed my script to minimal basic and it still gives...me same…

updated 12.8 years ago • Atul Kakrana

div class="preformatted">Hi all, I am scanning a geneset for all the Mmusculus motifs and comparing their enrichment to genomic background. I am using MotifDb...package to retrieve motifs and PWMEnrich for doing motif enrichment. I am getting error in the below code- 1). Get all motifs in Mmusculus from MotifDb in transfac format- In this step when exporting the motifs...as TRANSFAC format I …

BSgenome convert BSgenome PWMEnrich MotifDb

updated 11.4 years ago • deepti anand

res2 <- flowClust(mydata2, varNames=c("var1", "var3"), K=1:6, B=100) "Error in if (M == 0) label else maxLabel[[M]] : argument has length 0" I tried to decrease the number of K, as this error did not appear when...res2 <- flowClust(mydata2, varNames=c("var1", "var2", "var3"), K=1:4, B=100) And again the same error as above. This time it only works with up to K=1:3, and again the …

Clustering flowClust Clustering flowClust

updated 13.8 years ago • Anja Mirenska

working through the example in the documentation 'Text Description of affy' I receive the following errors with regard to loading the example data: > data(listcel) Error: restore file may be from a newer version of R -- no data loaded...gt; data(CDF.example) Error: restore file may be from a newer version of R -- no data loaded > I can generate the same error via: > load("…

cdf cdf

updated 23.5 years ago • Carleton Garrett

edgeR analysis, as I would like to try it with RUVSeq.  However, I am getting the following errors when I attempt to use the edgeR estimateGLMCommonDisp function: Error in mglmLevenberg(y, design = design, dispersion...dispersion, offset = offset,  :   BLAS/LAPACK routine 'DSYRK ' gave error code -10 If I use estimateCommonDisp instead, it works just fine, so I don…

glm edger lapack segfault ruvseq

updated 10.5 years ago • Mark.Rogers

<div class="preformatted">Got rid of the error after R was restarted. Puhong ----- Original Message ----- From: Puhong Gao To: bioconductor@stat.math.ethz.ch Sent: Thursday, March...div class="preformatted">Got rid of the error after R was restarted. Puhong ----- Original Message ----- From: Puhong Gao To: bioconductor@stat.math.ethz.ch Sent: Thursday...17, 2005 2:27 PM …

updated 20.9 years ago • Puhong Gao

in getZScores, I've ended up with nice-looking normal q-q plots, and the plotFits plots for all four samples show the expected interactions between my viewpoint enhancer and fragments at the target promoter and...an adjacent enhancer. However, I can't get plotZScores to work at all - I keep getting the following cryptic error: <pre> > plotZScores(fcf1[,c("viewpoint1_DMSO_1", "view…

fourcseq

updated 8.5 years ago • rustavo

sample but 184 patient samples. So, It has 186 columns (no technical replicates) and 20500 rows for all the genes. I am trying to get log2fold change data from this using deseq2. To begin my analysis I have extracted four patient...lt;-res\[order(res$padj),\] But, once I get to the ddsHTSeq function, it shows the following error: Error in Ops.factor(a$V1, l\[\[1\]\]$V1) :&n…

deseq2 cancer R

updated 8.4 years ago • dorothy.jrobbert

target or genes objects using the first menu (where the .raw name is entered) I get the following error from R (1.8.0): Error in structure(.External("dotTclObjv", objv, PACKAGE = "tcltk"), class = "tclObj") : [tcl] wrong # args: should be ".36.1.4.1.2...Thanks & regards, Casper _________________________________________________________________ Fĺ alle de nye og sjove ikoner med …

updated 22.2 years ago • Casper Frederiksen

Hi all, I am trying to run DESEQ on a merged counts file generated by HTSEQ. I am receiving the follow error message: Error in validObject

deseq2

updated 5.4 years ago • huck.thornton

<div class="preformatted"> Hi all, Could anyone give a hint on where to look to solve this problem? I am doing a loess normalization using a subset of genes that...<div class="preformatted"> Hi all, Could anyone give a hint on where to look to solve this problem? I am doing a loess normalization using a subset of genes that don?t change. I get the following errors. > test2…

Normalization limma marray Normalization limma marray

updated 21.2 years ago • M Inmaculada Barrasa

div class="preformatted">Hi All I am using GEOquery package to convert the dataset into expression set..But i m getting the following error.Here my script...lt;- getGEO(filename="/home/reemas/Desktop/GDS2821.soft.gz") eset <- GDS2eSet(gds,do.log2=TRUE) Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) : cannot open URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/annotation

convert GEOquery convert GEOquery

updated 15.1 years ago • Reema Singh

div class="preformatted">Hello, Iâm getting an error message when trying to run csHeatmap from CummerBund. All other functions are working fine so Iâm thinking that a required...that might be. Iâm not seeing any documentation out there that has this specific problem. The error seems to be common but I canât find the package that might not be there. All other required packages (fro…

cummeRbund cummeRbund

updated 13.2 years ago • Creasy, Todd

sep="_" ), intgroup = "group", force = T)</pre> I get an error message: <pre> Error in prepdata(expressionset, intgroup = intgroup, do.logtransform = do.logtransform) : all elements of...expressionset = try(as(expressionset, conversions[i])) if (is(expressionset, "try-error")) { stop(sprintf("The argument '…

arrayqualitymetrics R

updated 8.1 years ago • abf

Bioconductor User Group, I have installed affylmGUI on a PC and upon opening it Igot the error message Error message: Error in eval(expr,envir,enclos):Object "plot Options" not found. Can this error stop the program...the lady who wants his money is going to tell everybody that Fred gambles and it is going to be in all the papers in Middlemarch." Rose Friedman, age 8 </div

Cancer affylmGUI Cancer affylmGUI

updated 20.5 years ago • Richard Friedman

What are the expected upper limits of standard error values when using the limpa pipeline? I am analysing proteomics data from a control cohort and was surprised to see...What are the expected upper limits of standard error values when using the limpa pipeline? I am analysing proteomics data from a control cohort and was surprised to see a...number of standard error values just under 4. A…

limpa

updated 7 weeks ago • broadbentj

Hi all, Would you please suggest what wrong in this case? I pretty much run the same code as before. Thank you so much. result <- dba...dba.analyze(result) result <- dba.plotProfile(result) Generating report-based DBA object... Error: No valid contrasts/methods specified. And I don't know why my plot from `dba.plotProfile()` haven't analyzed. Would you help...0 I don't …

DiffBind

updated 2.5 years ago • Chris

<div class="preformatted"> Dear BioC users, I'm using LimmaGUI in R2.7 to analyse my microarray (miRNA exiqon v.10.0) experiments... But I'm not be able to solve this type of error that appearing constantly when I try to compute the linear model fit, particularly this error ever appears when I include in the model only the genes and excluding the controls. I made for this a specific SpotTy…

Microarray limmaGUI Microarray limmaGUI

updated 17.6 years ago • bzzandrew@interfree.it