Bioconductor Forum

Dear all, I have been trying to run a few examples using proteomics data and I have been getting the follow error message below. Could...gt;library("RforProteomics") Loading required package: MSnbase Loading required package: mzR Error: package or namespace load failed for ‘mzR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package...called ‘ncdf4’ Er…

proteomics error

updated 6.9 years ago • pdaltron

div class="preformatted">Hi all, I am using the unique(x) function with a DNAStringSet in one of my own functions. Recently my function has started returning...an error, and I am not sure what changed. The same line of code works fine in the R Console, just not in my function. I am using the function...as: myDNAStringSet <- unique(myDNAStringSet) When I run my function the error r…

Biostrings Biostrings

updated 15.8 years ago • Erik Wright

<div class="preformatted">Dear all, Since upgrading to the latest version of Bioconductor, I am having problems using the package arrayQualityMetrics because...div class="preformatted">Dear all, Since upgrading to the latest version of Bioconductor, I am having problems using the package arrayQualityMetrics...MLL", force = TRUE, do.logtransform…

arrayQualityMetrics arrayQualityMetrics

updated 15.2 years ago • James F. Reid

class="preformatted">Hello! I am trying to optimize my data processing with xps. I am getting an error when using the normalize function. It could be due to improper switches. here is the error: > data_norm <- normalize(data_bkgrd...Normalize_Step2", filedir=outdir, tmpdir="", update = FALSE, select = "pmonly", exonlevel="all", method="mean", option = "transcript:all", logbase…

Normalization PROcess xps Normalization PROcess xps

updated 11.5 years ago • Matthew Thornton

div class="preformatted">Dear all, I am getting a strange error this morning from Bioconductor. I am trying to connect from different servers and I'm still...getting the same error. Are there some database connection problems from Bioconductor? Error: Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id...ensembl_exon : Query ERROR: caught BioMart::Exception::Database: Could not con…

updated 12.7 years ago • methylUser

<div class="preformatted"> Hi All, I'm having a problem that has been mentioned here before but I'm not sure how to fix it. I tried to load flowQ and got: Error : .onAttach failed in attachNamespace() for 'flowQ', details: call: mysys("convert -list configure", intern = TRUE, ignore.stderr = TRUE) error: error in running command In addition: Warning messages: 1: replacing previous imp…

flowQ flowQ

updated 12.9 years ago • Guest User

I have just updated my BASiNET package and i received this error: <pre> ERROR: dependencies RWeka, rmcfs are not available for package BASiNET How can I fix it error? Because in my desktop...I install all dependencies that my package need. Is it possible to download dependencies directly from CRAN? How can I do this?</pre> Thank

dependencies error

updated 8.1 years ago • ericaugustoito

Hi all, I am fairly new to bioconductor packages but have had some experience in R. My R version is 2022.07.2 so it is the latest...Hi all, I am fairly new to bioconductor packages but have had some experience in R. My R version is 2022.07.2 so it is the latest. When...trying to load DMRcate library, I am getting the same error over and over again and I have tried to uninstall package and re…

DMRcate

updated 2.9 years ago • Bazingastats

topGO I try to follow the associated [vignette] [1], however I run into a problem of not finding the ALL library which is necessary in section 3.1 Data preparation. Please see below the steps I followed from the vignette and...lattice, MASS, nlme, nnet, spatial, survival Old packages: 'openxlsx', 'tidyr' Update all/some/none? [a/s/n]: a There are binary versions available but…

topGO

updated 5.7 years ago • vladimir.vinarsky

Dear all, I would like to filter the SNPs of a VCF file so to extract only SNPs distant of _X_ kb between each other. I do not see any built...in function to perform this kind of filtering so aimed at writing a filter rule to achieve it and pass it through the filterVcf function of the VariantAnnotation package. However, the kind of function

variantannotation

updated 11.0 years ago • remi.tournebize

div class="preformatted">Hi All, i've been trying to build BioC packages on macosx, but i can't get it to work. i got rid of fink and installed the g77 that comes...Frameworks/R.framework/Resources/etc/Frameworks/Makeconf: No such file or directory make: *** No rule to make target `/Library/Frameworks/R.framework/Resources/etc/Frameworks/Makeconf'. Stop. chmod: /private/tmp/Rinst1800553001

updated 19.8 years ago • Benilton Carvalho

Dear all, please could someone share if there is ANY RULE for making CIRCULAR PLOTS in GGBIO of ONLY CHROMOSOMAL SEGMENTS function

ggbio granges

updated 10.5 years ago • Bogdan

version is 4.0.3 and my biomaRt is up to date. My problem is I can’t use the function “getBM” in all of the ways. The error log is "Error in loadNamespace(name) : there is no package called ‘withr’ ”, which I can’t found the package...withr” to support this function. I have tried many codes to align gene profile with my data, but all failed. The error code was always shown "Error in loadNam…

biomaRt annotationTools

updated 5.0 years ago • niyamurry

div class="preformatted">Hi all, I am unable to access a series file even though I get a message that it saved to a local directory, albeit with an error message...sep = "\t", header = FALSE, nrows = nseries) : seek on a gzfile connection returned an internal error 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : seek on a gzfile connection returned an internal error …

GEOquery GEOquery

updated 14.3 years ago • Voke AO

plate were indeed 4 96 plates. Detector column was created for the first sample, and copy-pasted for all the remaining 15, so the detector names are the same. I've checked for spaces in the detector names or between the name and...C3 BMP1 27.33528 196 C3 BMP2 29.18772 > qPCRBatch.taqman <- read.qPCR(taqman) Error in .read.qPCR(filename, verbose) : File incorrect, m…

Read.qPCR error detectors

updated 10.0 years ago • Elena Serrano

condition <- as.factor(Metadata$condition) countData<- data.frame(readcount_matrix) countData all(rownames(Metadata) %in% colnames(countData)) countData<- countData[,-1] all(rownames(Metadata) == colnames(countData)) ``` #problematic...dds <- DESeqDataSetFromMatrix(countData = countData, colData = Metadata, design= ~condition)``` #ERROR Error in DESeqDataSet(se, de…

BiocGenerics DESeq2 DEGreport RNASeqData DEG

updated 3.5 years ago • Diya

Hi, I came across an error when building the TxDb from GFF as follow: __txdb <- makeTxDbFromGFF(gfffile, format="gff")__ _Import genomic features...file as a GRanges object ... OK_ _Prepare the 'metadata' data frame ... OK_ _Make the TxDb object ... Error in .get\_cds\_IDX(type, phase) : _ _ the "phase" metadata column must contain 0, 1, or 2, for all the __…

maketxdbfromgff

updated 8.0 years ago • bright602

with a white-space delimited file describing my samples called "covdesc" as suggested and have all the CEL files in the same directory I have loaded simpleaffy library and tried to read in the data. I get an error that has...mentioned but couldn?t find the solution in the Bioconductor Archives. This is what I type and the error > raw.data <- read.affy() Error in file(file, "r") : …

simpleaffy simpleaffy

updated 21.5 years ago • kfbargad@lg.ehu.es

Hi Julie, When I use CRISPRseek to predict off-target sites of Sp gRNA. I keep getting an error like this: "\[1\] "MY\_ERROR:   Error in library(GeneRfold): there is no package called ‘GeneRfold’\\n" Done. Please check output...Hi Julie, When I use CRISPRseek to predict off-target sites of Sp gRNA. I keep getting an error like this: "\[1\] "MY\_ERROR:   Error in library(G…

crisprseek

updated 9.8 years ago • Daniel

    0   <a name="86137"></a> [![gravatar for tarek.mohamed](https://secure.gravatar.com/avatar/a1153976bb5d406f3002a65f0ece23fe?s=82&d=identicon)](https://support.bioconductor.org/u/9489/) 56 minutes ago by [tarek.mohamed](https://support.bioconductor.org/u/9489/) • __0__   Hi, I am trying to use topgo to do GO ana…

topgo rnaseq

updated 9.4 years ago • tarek.mohamed

Run LFQ workflow of DEP package data_results <- LFQ(comparison_table, expdesign, type = "all", name = "description", alpha = 0.05, lfc = 1) When running the code, I get errors like : Error: 'Protein.IDs' is not a column in 'comparison_table...Error: 'Gene.names' is not a column in 'comparison_table'. These errors indicate that these arguments are required for the code...fun = …

LFQ R DEP error

updated 2.8 years ago • aymanreffai

<div class="preformatted"> Hi - I'm getting the following error when I try to do rma on loaded CEL data: > datafiles <- ReadAffy() > procinfo <- rma(datafiles) Note: You did not specify a...div class="preformatted"> Hi - I'm getting the following error when I try to do rma on loaded CEL data: > datafiles <- ReadAffy() > procinfo &l…

updated 22.1 years ago • Paul Grosu

div class="preformatted">Hi all: I'm new to R and Bioconductor. I'm trying to use makecdfenv package to create an environment for tiling arrays on Windows...This is the error I get: > make.cdf.package("arabidopsis_tlgF") Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) : Unable to

cdf makecdfenv cdf makecdfenv

updated 20.8 years ago • Ambika Sundaresan

Hi, all i am a so new to R bioconductor, now i am trying to download the data of GSE22216 from NCBI GEO data base. so i write the following...script in R. gset2<-getGEO("GSE22216") however , unfortunately the error message comes out, and i cannot solve this . Error in function (type, msg, asError = TRUE)  :   Failed to connect to [ftp.ncbi.nlm.nih.gov

getgeo geoquery

updated 10.0 years ago • maedakus

Hi all, I've just started to set up a workflow in IsoformSwitchAnalyzer, version 2.1.2. I'm having trouble with the analyzePFAM...aSwitchList, pathToPFAMresultFile = "pfam_out.txt", showProgress=FALSE ) Output: Error in h(simpleError(msg, call)) : err…

IsoformSwitchAnalyzeR

updated 2.6 years ago • Callum

div class="preformatted">Dear all, I think it's better to post here, instead on r-help. It's about MedlineR package in R; I receive the following error message when...using "getAmatrix" (co-occurance matrix between terms in PubMed) command: Error in xmlTreeParse(file = query, isURL = T) : error in creating parser for http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi...db=pubm…

updated 20.1 years ago • Andrej Kastrin

analysis of differential transcript usage following Salmon quantification. When I run: > all(rownames(cts) %in% txdf$TXNAME) It gives FALSE rather than TRUE. I have checked that all row names are unique in my salmon quantification...Dem1_rep1.quant)) > unique(Dem1_rep1.quant[dups]) length(dups) This gave zero duplicates for all of the quantification files. What co…

DRIMSeq tximport txdb Salmon

updated 5.4 years ago • Charlotte

div class="preformatted">Dear All, I was using GEOquery package After doing required steps I did this probesets <- Table(GPLList(gse6901)[[1]])$ID > data.matrix...x) { + tab <- Table(x) + mymatch <- match(probesets, tab$ID_REF) + return(tab$VALUE[mymatch]) + }))) Error in log(c("27", "59.8", "34.1", "110.5", "130.3", "569.3", "210.5", : Non-numeric argument to…

GEOquery GEOquery

updated 17.4 years ago • hemant ritturaj

Hi guys i'm getting the following error for Rsubread buildindex. "ERROR: Input file 'hg19.fa' is not found or is not accessible. No index was built." The file exists...and I've given all file permissions. Please help &nbsp

rsubread

updated 9.1 years ago • sh24

that the main effects will be shrunk too much relative to the interaction terms? That "interaction rule" results in obtaining two different answers to the same question. E.g., I can present 2\*3 design with interaction as 1-way...2\*3 design the main effects are not shrunk. Why was it so necessary to introduce the "interaction rule"? Regards, Nik &nbsp

deseq2

updated 10.4 years ago • Nik Tuzov

null hypothesis and have p-values at or near 1. With these kinds of tests, is there any equivalent rule to the "null p-values are uniform" rule described above for tests against an more typical null hypothesis

edger limma deseq2 p-value distribution

updated 9.9 years ago • Ryan C. Thompson

My first objective was to generate all possible positions (start and end) for hgnc_symbol, using for that purpose "start_position" and "end_position" attributes...lt;- biomaRt::useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl") # generate all possible attributes with pattern "start_position" biomaRt::searchAttributes(human_ensembl, pattern = "start_position...matches exactly six…

biomaRt cdna keys gene_start

updated 5.0 years ago • bastien_chassagnol

div class="preformatted">Hi all, R2.1.1 for windows xp I'm getting an error when I try to output my fitted data (called fullfit): >write.fit(fullfit, results...NULL, FStat=NULL, file=?filename?, digits=2, adjust=?fdr?) Error in data.frame(tab, fit$genes, check.names = FALSE) : arguments imply differing number of rows: 32448, 0 Any notions? Thanks

updated 20.3 years ago • scholz@Ag.arizona.edu

Hello everyone, I'm facing a hard limit when building large single-cell atlases in R by merging multiple SingleCellExperiment objects. The process fails when the combined object would exceed 2^31 - 1 non-zero elements in its count matrix. This is a common issue when working with over ~1 million cells. I understand this limitation comes from the dgCMatrix class in the Matrix package, which uses…

SingleCellExperiment

updated 6 months ago • Fabian

I am processing a NanoString data set where all of the samples fail the 20% Gene detection count test.   (The NanoString kit contains only a few genes that applicable...In this case, running makeQCReport fails in `` centeredSampleClustering `` with the error : <pre> Generating QC report... Gene-wise counts in blank samples: main image... [1…

NanoStringQCPro

updated 9.5 years ago • Gregory Warnes

blacklist... Removed: 5 of 58439 intervals. Counting control reads for greylist... Blacklist error: Error in value[[3L]](cond): GreyListChIP error: Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6, ... first error: 'seqlengths...contains NAs or negative values ``` Applying the blacklist works all right but greylist fails due to BiocParallel errors. From googling, I learned ab…

DiffBind

updated 4.5 years ago • kwangbom

median of ratios normalization) and low count filtered. The geneset is downloaded from Msigdb (All genesets). I get the following error and I don't know what is the problem. gsva_path <- gsva(Xdata,genesets,method= "gsva",min.sz...with 40 cores |======================================================================| 100% Error in dimnames(x) <- dn : length of 'dimnames' […

software error

updated 5.3 years ago • ElaM

to analyse. I did the required Rstudio and R updates and then reinstalled SingleCellExperiment and all necessary packages were loaded. please don't shoot me, I have very little knowledge in R but I'm really trying here is my issue...lt;- read10xCounts("/local/..../10X_aggr/outs/count/filtered_feature_bc_matrix") ``` and I get this error from R ``` Error: BiocParallel errors 1 remote errors, ele…

read10xCounts DropletUtils

updated 3.0 years ago • fdumetz

Hi all. I am trying to download a GSE file from the Gene Expression Omnibus and I am encountering a new error. Since the bug is still...my_id <- "GSE12657" readr::local_edition(1) gse <- getGEO(my_id) sessionInfo( ) ``` Error in readBin(inn, what = raw(0L), size = 1L, n = BFR.SIZE) : error reading from the connection In addition: Warning message: In readBin...inc…

GEOquery GEO Gene

updated 4.2 years ago • Caitlin

div class="preformatted">Hello there, I am writing to ask for some help with an error I am getting in LimmaGUI. I am able to load in my data files with no problem and create an M box plot with no normalization...for all arrays, but when I go to plot an M box plot with either within norm and or between normalization I get the following errors

Normalization GO limmaGUI Normalization GO limmaGUI

updated 20.5 years ago • Brooke-Powell, Elizabeth

Hi all, I have been using ChAMP package conveniently. I recently re-installed R, version 4.1.2, and now I cannot use the GUI functions...I got the following error message Error in shinytheme("readable") : Valid themes are: . My ChAMP version is 2.24.0. How can I solve this problem? Thanks

ChAMP shiny ChAMPdata

updated 3.9 years ago • Mari

<div class="preformatted">Hi All, I am having problem with Bioconductor in getting it to read .CEL files that were run on HG-U133 Plus 2.0 I am getting the following error: > library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() …

updated 20.8 years ago • Soumyaroop Bhattacharya

<div class="preformatted">Hi all, I used functions of pairwise.filter and results.summary from simpleaffy package to do gene filtering and summarization: results <- pairwise.comparison(eset, var1,c(group1,group2), spots = data_cel) g_inten7 <- pairwise.filter(results,min.exp=1,min.exp.no=0,min.present.no=0,presen t.by.group=F,fc=0,tt=1);#trying to keep all genes …

Cancer hgu133a probe Cancer hgu133a probe

updated 20.6 years ago • Jack Zhu

Hello,  I am trying to collect information of all samples but i don't know how to get all information for all samples. I tired the following, is there a better way to do that ?&nbsp

geoquery r

updated 10.8 years ago • Nemo

source ("http://bioconductor.org/biocLite) biocLite ("biomaRt") but I get this erros (XML and RCurl): ERROR: configuration failed for package 'XML' * removing '/home/alyaa/R/x86_64-pc-linux-gnu-library/2.11/XML' During startup - Warning...C" * installing *source* package 'RCurl' ... checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package 'RCurl' * removing…

biomaRt biomaRt

updated 13.6 years ago • Alyaa Mahmoud

<div class="preformatted">Dear List Members, I am getting the following error when I run maQualityPlot(RGlist) in arrayQuality package. Error in seq.default(0, 1, length = min(17, maxcnt)) : length must be non-negative number In addition: Warning message: no finite arguments to max; returning -Inf I have all updated packages installed from the Bioconductor. How can I resolve this?…

updated 20.3 years ago • Khan, Sohail

<div class="preformatted"> Hi, I am using limma package on HuGene2.0st array. When I tried to remove the unannotated rows (NAs) after mapping probeID to gene names. Some significant gene lists I got have the differentially expressed genes, but some of gene lists have all of the unsignificantly expressed genes. The code I used as follows: cont.matrix <- makeContrasts( inter…

probe limma probe limma

updated 12.5 years ago • Guest User

div class="preformatted">Hello, I am working with ExomeCopy, and I cannot get past this error: fit.list <- lapply(sample.names, runExomeCopy, seqs) *Error in negLogLike(c(logit(goto.cnv), logit(goto.normal), beta.hat...I have followed the vignette as closely as possible.) There are some exons that have zero reads for all 7 samples. Could this be causing the error? And if so, how ca…

exomeCopy exomeCopy

updated 12.7 years ago • Kevin Lee

a pipeline that worked before for me). But in the ImportRdata step the program keep returning this error in the import GTF step. I've searched in many forums but apparently nobody reported this error. <error rlib_error_dots_nonempty...Error in `dplyr::full_join()`: ! `...` must be empty. ✖ Problematic argument: • all = TRUE Run `rlang::last_trace()` to see wher…

dplyr IsoformSwitchAnalyzeR

updated 2.8 years ago • ramon.dslps

div class="preformatted">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 Error in dyn.load(file, ...) : unable to load shared...Versions/2.6/ Resources/library/Rgraphviz/libs/ppc/Rgraphviz.so Reason: i…

updated 18.0 years ago • yan zhou

installed R 1.7.1 and tried analyzing my data by running rma via expresso and get the following error: > expresso(data,widget=TRUE) background correction: rma normalization: quantiles PM/MM correction : pmonly expression...values: medianpolish background correcting...done. normalizing...Error in apply(intensity(abatch)[pms, ], 1, function(x) all(!is.na(x))) : dim(X) must have a …

updated 22.6 years ago • Kelvin Yen

<div class="preformatted">Dear All, I have been downloaded the SAGEnhaft library an start to learn about it. I get the paper, as well. But, I am very confusing if I will need another software, eSAGE, SAGE2000, or another one, to do all post analysis on SAGE data set. I will have 4 data set from two experiments. Each experiments will generate two data set: one...div class="preformatted"&…

SAGE sagenhaft SAGE sagenhaft

updated 19.3 years ago • Marcelo Luiz de Laia

Hello All,     I am attempting to use the mas5calls function to get present/absent calls on a large collection of microarray...I will admit I am new to this type of analysis and am looking for some direction to correct the error I am receiving. My error is produced as follows: <pre> > callsESet <- mas5calls(affy_liver_qc) Getting probe level data...Comput…

mas5 affy mas5 affy mas5 mas5calls affy

updated 10.2 years ago • suarez.samuel

Hello I am trying to add my data to class SingleCellExperiment while doing so getting an error, When am trying add metadata info please help me is it a bug or I am doing anything wrong even though i have same number...Hello I am trying to add my data to class SingleCellExperiment while doing so getting an error, When am trying add metadata info please help me is it a bug or I am doing anything wr…

SingleCellExperiment scran scater

updated 3.8 years ago • Lucky

div class="preformatted"> Dear All, I am getting error for mzR constantly. Please help out. > library(Biobase) > library(BiocGenerics) > library(methods) &gt...library(Rcpp) > library(mzR) Error : .onLoad failed in loadNamespace() for 'mzR', details: call: value[[3L]](cond) error: failed to load module Ramp from package mzR...negative length vectors are not …

mzR mzR

updated 13.1 years ago • Guest User

of the samples even is one is not very good. I did two different things : the first time I set the rule that peaks must be in both replicates...that gaves me 1116 differential peaks. <pre> dba_chip_consensus <- dba.peakset...dba_chip, consensus=c(type),minOverlap=0.99) </pre> Then I apply the following rule : the peaks must be at least in one or the other replicate. It g…

diffbind

updated 8.3 years ago • ZheFrench

Hello, I would like to filter one vcf by selecting only SNVs and in addition, those that only match genomic coordinates of a provided GRanges. I know that the filterVcf() function of Variant Annotation can deal with those requirements by using the isSNV() function on filters and by selecting on param argument the ScanVcfParam option. However, when just selecting the SNV filter I got some mes…

VariantAnnotation filterVcf

updated 10.4 years ago • pau.puigdevall

Hi all,  I have been running into an error while running champ.CNA() on a single array and I don't know how to solve it. After running...effects. Batch effects may affect your dataset. Saving Copy Number information for each Sample Error in sort(abs(diff(genomdat)))\[1:n.keep\] :    only 0's may be mixed with negative subscripts traceback() shows this:&nb…

ChAMP champ copy number

updated 9.0 years ago • apmishra

with rma function, both from the developer package and the standard release. I have included the error below. All I did was ReadAffy on some cel files, and then I tried the rma function. > dataA AffyBatch object size of arrays...number of samples=18 number of genes=22283 annotation=hgu133a notes= > estA<-rma(dataA) Error in density(x, kernel = "epanechnikov", n = 2^14) : …

updated 22.8 years ago • Kristina Hanspers

Basically I want to extract all attributes for several genes ,  when I use the following as example, I get an error , would anyone know why? hsapiens\_inf...nbsp;                'arrayexpress','chembl'),mart = mart) Error in getBM(attributes = c("ensembl\_gene\_id", "ensembl\_transcript\_id",  :&nbs…

biomart

updated 7.1 years ago • Bioinformatics