Bioconductor Forum

call to combineTests below fails: <pre> > tabcom <- combineTests(merged$id, results$table) Error: length(ids) == nrow(tab) is not TRUE > length(merged$id) [1] 14051634 > nrow(results$table) [1] 120695</pre> When I get this error, what...and it works on many datasets, but fails on one particular for some reason): <pre> data = readRDS(snakem…

csaw

updated 8.3 years ago • endrebak85

Hello, I realized that when I run Deseq2 in the terminal, it gives me a different result (different values in the res table except for baseMean) compare to when I run in with Snakemake (I was able to reproduce the same issue also on a different computer). However, when I use only one CPU for R in terminal ```taskset --cpu-list 1 R``` it gives me the same results as with Snakemake. My code: ``…

DESeq2

updated 5.1 years ago • David

div class="preformatted"> Below is a makefile I wrote to download and install all available R packages from the CRAN and BioConductor package repositories. The primary advantage of using this makefile...packages. I hope that this script may be useful to other folks. -Greg # Download and install all available R packages from the CRAN and Bioconductor # package repositories # RCMD ?= R-1.9.0…

updated 21.8 years ago • Warnes, Gregory R

<div class="preformatted">What is the rule of the MM desing on the Affymetrix array? I think it is a one-basepair change in the middle, but how exactly? A-> C T->G, C->T...div class="preformatted">What is the rule of the MM desing on the Affymetrix array? I think it is a one-basepair change in the middle, but how exactly? A-> C T->G, C-&gt

updated 18.2 years ago • Simon Lin

Dear All, I am writing a script that uses STRINGdb library. When I call: <pre> enrichmentGO_Process <- string_db$get_enrichment...Dear All, I am writing a script that uses STRINGdb library. When I call: <pre> enrichmentGO_Process <- string_db$get_enrichment(genes...STRING_id, category = "Process", methodMT = "fdr", iea = TRUE)</pre> I get an error: <pre&…

STRINGdb stringdb gene set enrichment analysis software error go

updated 7.1 years ago • wsciekly.maciek

Hi Team, In our Azure environment NSG outbound rules are not allowed to public websites from any Linux VM. We have allowed specific IP ranges to allow https://bioconductor.org

software error

updated 6.0 years ago • vkatakwar

using a bacterial genome and GTF annotation files downloaded from GenBank. When run, the following error message is generated: ``` Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame...Make the TxDb object ... Error in .make_splicings(exons, cds, stop_codons) : some CDS cannot be mapped to an exon Calls: makeTxDbFromGFF -> makeTxDbFromG…

GenomicFeatures

updated 3.6 years ago • rsnorman

I am trying to access the ALL library and ALL data set. When I enter the following commands, I run into errors. How do I resolve this?  <pre> > source("https...biocLite.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help > biocLite("ALL") BioC_mirror: https://bioconductor.org Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31…

bioconductor R library software error ALL library

updated 9.0 years ago • alyssa.ylescu

div class="preformatted"> Hi, I need to obtain information via biomaRt for all members of interleukin. Trying the following command failed, apparently, getBM doesn't support regexp. I could download...all the gene names and filter locally, but this will stress the hosting server and prolong communication time. getBM(attributes

biomaRt biomaRt

updated 17.1 years ago • Daren Tan

Hi everyone I am trying to port my 16S workflow that uses dada2, phyloseq and DECIPHER onto a Linux server. I have split the jobs up and am using snakemake to run through them. Seems fine. When I go onto the server, I use conda to create a new environment and then install snakemake and R v4.0.3 into it. ``` # first install mamba as its faster for installing than conda conda install -c conda-fo…

dada2 conda phyloseq

updated 4.8 years ago • Daniel

All other parts of the ATACseqQC package works, but when the shiftGAlignmentsList command is ran to shift the reads and split...the BAM files, the command fails with the following error: (all(elementNROWS)>3) is not TRUE. However, in R, when I run that line, it returns as TRUE. What is the exact error the script

ATACseqQC ATAC ATACseq software error Tutorial

updated 6.6 years ago • mbasam

Hi, An error occurred when I used the prePdata function: all (unlist (md_cols)% in% names (md)) is not TRUE: > sce <- prepData(samp, Panel, Sample_sheet...features = Panel$fcs_colname) Error in prepData(samp, Panel, Sample_sheet, features = Panel$fcs_colname) : all(unlist(md_cols) %in% names(md)) is not TRUE I checked...Sample_ sheet$file_ The file name of nam…

cytofWorkflow

updated 2.9 years ago • shuangshuang

list.celfiles("expressionData", full.names=TRUE) Data <- read.celfiles(celFiles) I got this error: All the CEL files must be of the same type. Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE All CEL

updated 12.2 years ago • Jerry Cholo

Hi all! I'm using cn.MOPs package, but, in the last step, I have an error message. This are my steps: <pre> > BAMFiles<-list.files(pattern...chrM Starting segmentation algorithm... Using "fastseg" for segmentation. Error in if (all(segMedianT == 0)) { : missing value where is request TRUE/FALSE Inoltre: Warning message…

cn.mops cnv

updated 8.1 years ago • martyferr90

to be working well, I have run into an issue where the estimatesizefactors is returning a strange error. Input is: <pre> dds <- dds[ rowSums(counts(dds)) > 1, ] cts <- counts(dds) geoMeans <- apply(cts, 1, function(row) if (all(row == 0)) 0 else exp...row[row != 0])))) dds <- estimateSizeFactors(dds, geoMeans=geoMeans)</pre> This returns …

deseq2 error R estimatesizefactors zero

updated 8.1 years ago • abhishek.yedugondla

All State To State Auto Transport][1] is the nation's premier provider of nationwide door-to-door auto transportation services

alabaster.schemas

updated 20 months ago • All State To State Auto Transport

I have 6 samples, 3 sets of 2 replicates. Not sure why the error is coming up. Something that seems off is that it says 'computing metrics for 10 samples when I only have 6. ```r chipObj &lt...I have 6 samples, 3 sets of 2 replicates. Not sure why the error is coming up. Something that seems off is that it says 'computing metrics for 10 samples when I only have 6. ```r chipObj &…

ChIPQC

updated 4.7 years ago • Jonah

normalized samples to a common single-cell-experiment, or whether I should normalize over all three samples together. Initially, I thought that I should do it for each sample separately, because in the OSCA chapter...books/3.15/OSCA.multisample/integrating-datasets.html#quick-start) they say " As a general rule, these upstream processing steps (quality control and normalization) should be …

scran Normalization scRNA BatchEffect

updated 3.0 years ago • r_grau

Dear Dr Klambauer, I met an error when using singlecn.mops. At the modelling part, it runs well at the beginning, but when operating on NW_020228985.1...an error occurred as below, but it runs well when I try it using the same reference genome. Will it matter if the reference genome...NW_020228924.1 Reference sequence: NW_020228957.1 Reference sequence: NW_020228985.1 Error i…

cnmops cn.mops error

updated 6.6 years ago • s1812756

div class="preformatted">When I try to run Greg's installer script I immediately get a syntax error for the command "RCMD ?= R-1.9.0". I am running 1.9.0 on Windows XP. Am I doing something wrong? Mark Mark W. Kimpel MD Department...Warnes, Gregory R" <gregory_r_warnes@groton.pfizer.com> Subject: [BioC] Makefile for installing all available packages To: "R-Help (E-mail)" <r-help@st…

updated 21.8 years ago • Kimpel, Mark W

BiocManager::install("topGO") The installation seems to have been successful and returned no errors, but it says... The downloaded source packages are in ‘/tmp/RtmpSyYduw/downloaded_packages’ Updating HTML index of packages...done Then, I'm immediately asked to load the libraries... library(topGO) library(ALL) data(ALL) data(geneList) geneL…

topGO software error

updated 6.6 years ago • Raito92

s2c$sample $ txi <- tximport(files, type="rsem", txIn=F, txOut=F) However, I get an error message saying "all(file.exists(files)) is not TRUE" and cannot proceed. What is the problem? [1]: /media/images/1963841e-3e0b

Linux R tximport

updated 3.9 years ago • nakane_clan

Homoscedasticity,Independence, and Normality etc, quantitative PCR data may not necessarily meet all these criteria. So my question is: Is there a need or general principle/rule to assess whether the data types/distribution

limma highthroughputassays R

updated 4.2 years ago • Ming

div class="preformatted"> unable to install "ALL",please help me . -- output of sessionInfo(): output: biocLite("ALL") BioC_mirror: http://bioconductor.org Using Bioconductor version...2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'ALL' trying URL 'http://bioconductor.org/packages/2.13/data/experiment/bin/ windows/contrib/3.0/ALL_1.4.16.zip' Content type...application…

updated 12.2 years ago • Guest User

Hi again, Now I've used the new gcrma I've noticed something strange, which is probably an error somewhere, maybe not with gcrma itself. When I computed gcrma with my old R devel 2.0, BioC devel (gcrma 1.1.1, ATH1cdf 1.4.3...1.0.9, affy 1.5.2) I got 'sensible' expression estimates. Using the current R2.0, BioC 1.5 (all others above look the same except matchprobes is now 1.0.12 and affy 1.5.8) …

cdf affy gcrma matchprobes cdf affy gcrma matchprobes

updated 21.2 years ago • Matthew Hannah

been trying to install bioconductor 2.5 packages using biocLite and keep receiving the following error message: package 'KEGG.db' successfully unpacked and MD5 sums checked package 'AnnotationDbi' successfully unpacked...and MD5 sums checked Error in normalizePath(path) : path[1]="C:\Program Files\R\R-2.10.1\library/AnnotationDbi": The system cannot find the file specified...BioC, *>* *…

updated 15.9 years ago • Eric Bremer

1 537151_1_25 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq: 9.25;count:01;rules:0000;score:0812 2 537151_1_27 BLOCK1 interval rank target_tm:76.00;probe_tm:75.70;freq:10.71;count:01;rules:0000;score...08 28 3 537151_1_29 BLOCK1 interval rank target_tm:76.00;probe_tm:86.60;freq: 3.31;count:01;rules:0000;score:0706 4 537151_1_31 BLOCK1 interval rank target_tm…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.4 years ago • Nitesh Turaga

div class="preformatted">Dear All I am using RSPerl to call R from Perl in my workstation with fedora core -5, for which i used ./configure --enable-R-shlib option...while the same package i am trying to install in HPC cluster with centos showing the following error messeges. in make check ---------------------------Messege displayed on make check ---------------------------------------------…

updated 17.3 years ago • ALok

I receive the following error when I try to create a txdb from a gff file that I imported into GRanges: <pre> > GenomicFeatures::makeTxDbFromGRanges...test) Error in .get_cds_IDX(type, phase) : the "phase" metadata column must contain 0, 1, or 2, for all the CDS features</pre> However, when I check

genomicranges

updated 7.4 years ago • bbrink

operational without the suggested packages, resulting in a lot of manual dependency resolution. The rule seems to be "Don't call my really useful functions without manually resolving all my possible dependencies." Can we move...all "Suggests" into "Depends" and deprecate the Suggests metadata? -- output of sessionInfo(): . -- Sent via the guest posting facility

updated 13.1 years ago • Guest User

I have been using DMRcate for quite sometime now and the code I have runs absolutely perfectly in all my datasets besides one, which throws me the error: Error in approx(x = x, y = i, xout = xout, rule = 2) : need at least two non-NA values to...for this data and makes me wonder if it is due to the low number of DMPs? Does anyone knows why this error occurs? ```r DMR <- dmrcate…

DNAMethylation DMRcate

updated 21 months ago • Macsue

bg_chrX = ballgown(dataDir = "ballgown", samplePattern = "ERR", pData = pheno_data) The error I get is Fri Jan 25 12:20:27 2019: Reading linking tables Fri Jan 25 12:20:27 2019: Reading intron data files Fri Jan 25 12:20...12:20:29 2019: Reading transcript data files Fri Jan 25 12:20:29 2019: Merging transcript data Error in ballgown(dataDir = "ballgown", samplePat…

software error ballgown

updated 7.0 years ago • aaubry89

When I am importing the files using the DESeqDataSetFromHTSeqCount function, the script throws an error : all samples have 0 counts for all genes. check the counting script. I am unable to figure as in what is lacking or what I missed...output # please also include the results of running the following in an R session sessionInfo( ) ``` Error in DESeqDataSet(se, design = design, ignoreRank) : …

DESeq2 TCGAWorkflowData RNASeq

updated 4.5 years ago • 2K18-BT-034 Saksham

Hi, I just started a differential expression analysis using DESeq2 with a count dataset. There are two cellines in which I want to detect the DE ; a radiated one and a control one. Now I have used DESeq2 and DESeqDataSetFromMatrix before and they have always worked fine for me, but now for some reason when I want to run DESeqDataSetFromMatrix, the function displays an error mes…

deseq2 deseq counts rnaseq differential gene expression

updated 9.7 years ago • wannes.nauwynck

in R version 2.8 worked fine, however, after updating to R2.11.1 I run into problems and the error message "Error in if (x <= tightCutoff) return("P") else if (x > looseCutoff) return("A") else return("M") : missing value where TRUE...function used in pa.calls() has changed in R 2.9.1: "approxfun() and approx() now accept a 'rule' of length two, for easy specification of differe…

affy affy

updated 15.4 years ago • Samuel Wuest

Hi all, I'm using DESeq2 for the first time and ran into some problems during the LFC shrinkage step. I got this error when I tried...Hi all, I'm using DESeq2 for the first time and ran into some problems during the LFC shrinkage step. I got this error when I tried to run the process function "lfcShrink()": using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014). Note that t…

deseq2 software error

updated 5.8 years ago • junli1988

materials/data/tutorial/cross_platform/tutorial.html When I run the following code, I get an error: ``` ################ combine EPIC and 450k ############## DIR_DATASETS<-"~/Downloads/" # Let us now load each individual RnBSet object: PLATFORMS<-c("450k...gt; rnb.set.arrays<-combine(rnb.sets[["450k"]], rnb.sets[["EPIC"]], type="common") Error in do.call(combine,…

RnBeads Rnbeads2.0 RnBeads2

updated 4.8 years ago • D

pd.mapping250k.nsp") chips Mapping250K_Nsp Mendel_Nsp 2 1 Error in justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate = recalibrate, : All the CEL files must be of the same...1: What is Mendel_nsp? It looks like one of the file is Mendel_nsp Question 2: Is this an error that I can by pass with CRLMM and how? or is it an error that I sh…

SNP crlmm SNP crlmm

updated 16.6 years ago • mcoyne@boninc.com

Good day, Please help with batch option in Deseq2, I have the error below and can't understand the problem as for me my METADATA_RAT has nessesary columns txi.salmon_rat ENSRNOG00000000070...lt;- DESeqDataSetFromTximport(txi.salmon_rat, colData = coldata_rat, design = ~ batch + condition) Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be…

BatchQC batchinDeseq2. columnsincolData.

updated 20 months ago • Galina

example, for the lung abundance file, it has the transcripts listed for the kidney but with 0 for all of the abundance information. Then I sorted and filled both abundance files and the tx2gene map so they have the same transcripts...in the same order for all. I am still getting the error. I followed the steps from: https://bioconductor.org/packages/release/bioc/vignettes/tximport...file.path(…

tximport

updated 4.2 years ago • nicolette.sipperly

div class="preformatted">Hello all, I'm a new to bioconductor and encounter an error when I use oligo for the analysis of affymetrix mouse Gene 1.0 ST array. A...read.celfiles. No matter the files are ( mine or GEO one that had worked fine), now I always see an error as "All the CEL files must be of the same type. Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE"....…

BiocViews Annotation Organism biocViews oligo BiocViews BiocViews Annotation Organism

updated 14.6 years ago • Setsuko Sahara

on my datasets (5GB-8GB for each sample bam file), it needs very large memory but still produce errors. I find a post but without any solution. https://support.bioconductor.org/p/p132997/ I am not sure it is caused by my data...Sample: GM12890_Input_1.nodup.bam200 Sample: GM12891_Input_1.nodup.bam200 Error in DESeqDataSet(se, design = design, ignoreRank) : all samples have 0 counts for a…

dba.count DiffBind3

updated 3.9 years ago • yang

Cc: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: [BioC] limma all by all > > Hi, > I have microarray data from 10 different cell types. I want to identify > DEGs by an all cell type by all cell...just do an F-test. There are examples of this in the limma User's Guide. > and one cell type vs. all cell type compa…

Microarray limma Microarray limma

updated 11.7 years ago • Gordon Smyth

training.github.io/2018-June-RNA-Seq-Workshop/thursday/DE.html and some parts are showing errors or unexpected results. Despite the error below, I was able to run the next part of the limma DE gene analysis, but the result...was 0 downreg and 0 upreg genes. I suppose it may be due to the error below. It would be very much appreciated if someone could help. The data structure may…

GeoMx limma DifferentialExpression

updated 18 months ago • sophie00824

div class="preformatted">Hi, I run the example of read.HTSeqCounts() from DEXSeq, get following Error: Error: all(unlist(lapply(design, class)) == "factor") is not TRUE Any suggestion? Thanks in advance. Regards, Sheng code: library

DEXSeq DEXSeq

updated 13.4 years ago • sheng zhao

pre> Conumee error: Error in .local(query, ref, anno, ...) : query intensities not given for all probes.</pre>   This error results when I use  x

conumee

updated 4.7 years ago • yura.grabovska

and 1/1 will be 1 so I will set them somehow to a number that I will be able to plot the curve for all proteins.  and I got the following error  <pre> Fitting 3663 individual dose response curves to 3663 proteins. Error...missing value where TRUE/FALSE needed"</pre>   I want to obtain the curve fitting for all proteins and not only those that met the a…

tpp

updated 9.3 years ago • Bioinformatics

1): filterGtProp starting filter filtering 10000 records</pre> But then I receive the following error: <pre> Error in extractROWS(x, eval(filter, x)) : error in evaluating the argument 'i' in selecting a method for function 'extractROWS...Error in rule(envir) : promise already under evaluation: recursive default argument reference or earlier problems?</pre> Following...t…

variantannotation filtervcf

updated 10.2 years ago • TimothéeFlutre

<div class="preformatted">Dear all, I am trying to get familar with SAM. the Excel version does not seem to have the option to specify a value for s0 (the fudge factor...div class="preformatted">Dear all, I am trying to get familar with SAM. the Excel version does not seem to have the option to specify a value for s0 (the fudge...some values in terms of quantiles of the standard deviat…

siggenes ASSIGN siggenes ASSIGN

updated 21.4 years ago • Caimiao Wei

div class="preformatted">Dear All, This is my 1st post to bioconductor so please bear with me if I violate any rule. I want to do pathway analysis on my Mycobactirum

updated 13.4 years ago • ashwani Kumar

lt; b) return(1e50) return(2) } ``` In my understanding, it has the following effect. - All child nodes (terms) are always treated as more significant irrespective of actual p-values (and CASE 1 is impossible). - Thus...CASE 2), genes associated with all child nodes are always removed for an analyzed node (term). As a result, gene propagation based on the rule of path is reverted…

topGO weight01

updated 4.9 years ago • Vladimir

and classification algorithms in general. Is there a way to obtain the equation of a decision rule created when using MLInterfaces on a exprSet object? Specifically, I am using stat.diag.daB to implement DLDA. I would...like to apply the same decision rule to arrays from multiple datasets. Alternatively, if I define the same arrays as the learning set used as input to MLInterfaces...will it p…

Classification MLInterfaces Classification MLInterfaces

updated 19.2 years ago • mpg33@drexel.edu

div class="preformatted">Hi all, I have a problem with DESeq calculations. Error message: Error in FUN(newX[, i], ?): function "locfunc" unknown All my packages are...up to date and reinstalled. Does anybody know this error? I would be extremely Happy to hear about it soon, Philipp</div

DESeq DESeq

updated 13.3 years ago • Philipp Brand

analysis (iam a biologist with zero training in statistics and bioinformatics try to teach himself all the stuff). I tried already both options and DESeq2 gives me ~15 % less differential methylated sites. However Iam not sure...how to judge if I get ride of false postive or i simply loss positiv peaks. Is there a rule of thumbe when to use edgeR or DESeq2.   Thanks for any suggestion

diffbind medip-seq edger deseq2

updated 8.2 years ago • florian.noack

Now, I am trying to use diffbind for identifying differtial peaks. But I am have the following error whole running `dba.count`. I am not sure why I am having this. Any suggestions? Thank you > dbObj <- dba.count(dbObj, bUseSummarizeOverlaps...TRUE) Computing summits... Re-centering peaks... Reads will be counted as Paired-end. >Error in DESeqDataSet(se, design = desi…

DiffBind Genrich

updated 5.1 years ago • peris_baba

I am using DEXSeq to perform a DEU analysis on some bulk RNA-Seq data but I am getting some strange behavior. My data comes from a transgenic animal model, so I've introduced a custom gtf file for the transgene. I am able to follow the vignette for DEXSeq well, but I went back today to try and update my summarized experiment object with rowRanges because I realized this didn't get done the first …

DifferentialSplicing RNASeqData DEXSeq

updated 11 months ago • cftattersfield

SEQ_ID > >> 2 target_tm:76.00;probe_tm:77.60;freq: > >>9.25;count:01;rules:0000;score:0812 chr19:6588109-6599163 > >> 3 > >>target_tm:76.00;probe_tm:75.70;freq:10.71;count:01;rules:0000...83677266-83688611 > >> 4 target_tm:76.00;probe_tm:86.60;freq: > >>3.31;count:01;rul…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.4 years ago • Benilton Carvalho

meta).  One of my metadata columns is a factor with 5 levels (factors).  I want to do all pairwise comparisons for all 5 factor levels.   I've tried to do it this way: dds = DESeqDataSetFromMatrix(countData = otu...FALSE) The rownames in my metadata are the same as the colnames in the otu table, but I get an error: Error in FUN(X\[\[i\]\], ...) : &nbsp…

deseq2 contrast matrix

updated 8.9 years ago • natalie.hull

td> <p> </p> </td> <td> <p>I'm having issues creating the coldata frame. Below is my script and error.</p> <pre> <code>countdata <-read.table("~/Desktop/Internship/Extracted CP.Auto genes from RNASeq batch_1.txt",header=TRUE...row.names=colnames(countdata), condition))</code></pre> <p>After I input the last line…

deseq2 R genomics

updated 8.0 years ago • mokunf

on a number of pd.hugene.2.0.st samples (CEL files) and encountering the same error on two different machines with fresh installs of Bioconductor and arrayQualityMetrics, one with R 3.1.1 and another...arrayQualityMetrics(expressionset = mydata, force = T, do.logtransform = T) </pre> The error when running arrayQualityMetrics the first time gives <pre> The directory 'arra…

arrayqualitymetrics svg software error

updated 9.6 years ago • Paulo Nuin