Bioconductor Forum

chrY 　 done Calculating coverage Calculating Summits on chrY ..[1] 1 list Error in names(res) <- nms : 'names' attribute [8] must be the same length as the vector [6] In addition: Warning message: stop worker failed: 'clear_cluster

chipqc

updated 8.5 years ago • C T

it is ``` DataFrame with 3 rows and 3 columns chr pos strand <character> <integer> <character> cg00000292 chr16 28797601 + cg00002426 chr3 57718583 + cg00003994 chr7 15692387 + ``` While for the...it is ``` DataFrame with 3 rows and 3 columns chr…

IlluminaHumanMethylation27kanno.ilmn12.hg19

updated 4.8 years ago • yuabrahamliu

**1.)** EGSEA testing with report generation enabled consistently gives me the following error: Error in array(col.rgb[, i], dim(node.rgb)[3:1]) : negative length vectors are not allowed This error occurs for both the `report=TRUE` setting or using the manual S4 method `generateReport()` function...**1.)** EGSEA testing with report generation enabled consistently gives me the following erro…

egsea EGSEA123

updated 2.7 years ago • neilzhao

DESeq2) Time = rep(c("0h", "120h", "240h"), each = 2) Treat = c(rep("Control", 2), rep("Treat", 4)) nameD <- paste(Treat, Time, c(rep(LETTERS\[1:2\], 1), rep(LETTERS\[3:4\], 2)), sep = "\_") sampleInfo <- data.frame(row.names = nameD, Time = Time, Treat...more variables or interaction terms in the design formula are linear combinations of the others and must be removed

deseq2

updated 7.6 years ago • dryellaboina

<div class="preformatted">Dear List, I'm trying to filter some microRNA expression data generated on the Affymetrix miRNA 2.0 array platform before running the DE genes analysis. However, I get an error when I apply the nsFilter function in the genefilter package - see below: #### my script #### #Set working dir setwd("C:/Users/CEL") #produce a character vector of the names of the files …

miRNA Annotation microRNA BiocInstaller miRNA Annotation microRNA BiocInstaller

updated 14.1 years ago • Peter Davidsen

Chr1:711 Chr1:956 ... ChrM:366919 ChrM:366920 *Qustion: After used renameSeqlevels() to change chr name of vcf (Chr to chr), the rownames here are still old chr name. not sure if this will be the problem for predictCoding(). * rowData...values names(1): paramRangeID colnames(2): sample1_aln.sorted.bam sample2_aln.sorted.bam colData names(1): Samples > txdb TranscriptDb...gt;> seqSo…

Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation

updated 13.3 years ago • sun

mentioned that this is impossible without demanding expression in every sample, because filtering must me done unsupervised (= without knowledge of which condition is applied to each sample), before feeding the data to

edgeR RNAseq DE analysis gene filtering

updated 9.4 years ago • Mau

about the project, see [lab info][1]. **Qualifications:** ------------------- Applicants must have a Ph.D. in bioinformatics, computational biology, statistics, human genetics or related field, and a sound understanding...of biology, data science and statistical modeling. Must be proficient in statistical and programming languages such as R and Python, and familiar with Linux and high perfo…

Bioinformatics RNA-seq Postdoc Genomics Statistical model Job

updated 7.0 years ago • djawaheer

pre> aws ec2 copy-image --source-image-id ami-abd0b3bc --source-region us-east-1 --region us-west-1 --name "Bioconductor 3.3" An error occurred (InvalidRequest) when calling the CopyImage operation: You do not have permission...docs.aws.amazon.com/AWSEC2/latest/UserGuide/CopyingAMIs.html): <pre> The owner of the account must grant read permissions on the storage that backs the AMI,…

amazon cloud

updated 9.2 years ago • Thomas Sandmann

Avenue, Boston MA 02115, rm 536. Persons not already subscribed to the BiocBUG mailing list must register with me to attend the meeting. Just e-mail me with the names of all attendees you are registering. There will be...in Infectious Disease of Military Importance. =============== To access the Channing Lab, you must use Palace Road (parallel to Huntington Ave, just past the Mass College of A…

Microarray GUI Microarray GUI

updated 22.1 years ago • Vincent J. Carey, Jr.

extended = extended, verbose = verbose) :   The following specified files do not exist:character(0)\_Grn.idat, character(0)\_Grn.idat, character(0)\_Grn.idat, character(0)\_Grn.idat, character(0)\_Grn.idat, character...0)\_Grn.idat, character(0)\_Grn.idat, character(0)\_Grn.idat, character(0)\_Grn.idat, character(0)\_Grn.idat, character(0)\_Grn.idat, character...0)\_Grn.idat, characte…

minfi

updated 9.5 years ago • Biologist

PD")) to retrieve the result. However, I am wondering about the result from calling results(dds,name="ResponsePRCR") which is supposed to give us the individual effect and yet has the all the result columns, baseMean, log2FoldChange...What exactly is this "individual effect"? How do I interpret the result from using name option? What's the difference between using contrast and using name? Thanks …

DESeq2

updated 8.2 years ago • fkuo

me out. Best wishes, Marjolein.  > sc\_all <- SCseq(input\_merged\_all)  Error: vector memory exhausted (limit reached?)   > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86\_64-apple-darwin15.6.0

software error

updated 7.5 years ago • mdroog

same directory, and read them all. but I got the following error messages, Error: cannot allocate vector of size 3828 Kb What is the maximum size marray package can handle to read into R? Any suggestion is greatly appreciated...lt;<gu, joyce.vcf="">> -------------- next part -------------- A non-text attachment was scrubbed... Name: Gu, Joyce.vcf Type: text/x-vcard Size: 173 bytes D…

marray marray

updated 21.9 years ago • Gu, Joyce

not open file text.cel So to read specified files from a specified directory, one should give a vector of full path names: abatch <- ReadAffy(filenames=file.path(celpath,"text.cel")) Is this the recommended way to do it? Gordon

updated 21.4 years ago • Gordon Smyth

colnames to another ID's system, HUMAN_LLID by using the table. The colnames of x1 with the same names (in HUMAN_LLID) need to be averaged. Is there a good way to do it? I also put this question in bioconductor since I believe

convert convert

updated 19.2 years ago • Weiwei Shi

1): counts rownames(33602): AT1G01010 AT1G01020 ... ATMG01400 ATMG01410 rowData metadata column names(0): colnames(1): reads colData names(2): object records as I understand exptData is empty and there the counts should appear...lt;- exonsBy (TxDb.Athaliana.BioMart.plantsmart19, "gene") # Added correct Chr sizes and the same names than the samples >seqlengths(TAIR10_GRL) <- c(30427…

RNASeq Alignment biomaRt rtracklayer DESeq RNASeq Alignment biomaRt rtracklayer DESeq

updated 11.8 years ago • Guest User

other. To avoid this issue, I wished to plot only a few custom genes filtered based on the gene name. The key question is how would I do that in such a way that Txdb object makes its own filtered Txdb object which then I can...genes[gene.data$genes$gene_id %in% ranges.df[ranges.df$coverage == unique(ranges.df$coverage)[1],]$names] ``` 2. select() won't work here, but can I make it a custom T…

GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene

updated 2.7 years ago • Shreyash

div class="preformatted"> Is there a way for me to use Bioconductor to take a list of gene names and give me back a list of genomic sequences, preferably with the exons and introns easily differentiable (e.g. exons

updated 12.5 years ago • Guest User

lt;- exonsBy(txdb, by=c("gene")) bfl <- BamFileList(outpaths(args), yieldSize=50000, index=character()) multicoreParam <- MulticoreParam(workers=4); register(multicoreParam); registered() counteByg <- bplapply(bfl...seq(along=counteByg), function(x) assays(counteByg\[\[x\]\])$counts) rownames(countDFeByg) <- names(rowRanges(counteByg\[\[1\]\])); colnames(co…

cuffdiff sqlite

updated 8.1 years ago • handgabriel

Hi all, I am working with Agilent microarray data and trying to extract only the accession numbers from the output probe annotation. Basically I have a column detailing the probe as follows: ref|NM_004564|ref|PET112L:2131|mgc|BC130348:2158 ref|NM_007266|ref|XAB1:2255|mgc|BC007451:2239 mgc|BC034752:79 ref|NM_057094|ref|CRYBA2:-2513|ref|NM_005209:-2519|ref|NM_194302:45605 |mirna|hsa-mir-375:5790 .…

Microarray Annotation probe Microarray Annotation probe

updated 16.6 years ago • Hari Easwaran

between different groups (this is not array data and i'm not using limma). Any on what the error must be ? > mydata.eset ExpressionSet (storageMode: lockedEnvironment) assayData: 2754598 features, 3 samples element names

updated 15.0 years ago • David

Hi, I'm trying to change the font size of the gene name and increase the arrow head size. I've tried changing the cex and cex.id but it does'nt seem to be effecting the font size...Hi, I'm trying to change the font size of the gene name and increase the arrow head size. I've tried changing the cex and cex.id but it does'nt seem to be effecting the font size; for example below I set both to 30 w…

DMRcate Gviz

updated 4.1 years ago • Ahdee

EBTest(Data = ebvRna1, Conditions = condition1, sizeFactors = sizes, : Please add gene/isoform names to the data matrix** But I checked my Data by **str(ebvRna1)** **int [1:395, 1:20531] 2 2 2 2 2 2 2 2 2 2 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:20531...LOC100130426" "UBE2Q2P3" "UBE2Q2P3.1" "LOC149767" ...** It looks I have the gene names for my matrix. Doe…

EBSeq

updated 5.6 years ago • lli2

set IDs. This is after normalisation and linear model fitting. However when I try to apply gene names the error below occurs. Error in text.default(fit$coef[topGenes],fit$lods[topGenes], labels=substring(genelist[topGenes...labels' The volcano plot is produced but with no labels. Also the TopTable does not contain gene names or functions. This occurs with data files from two different chips.…

affylmGUI affylmGUI

updated 14.1 years ago • Guest User

genomdat)) genomdat <- as.matrix(genomdat) if (!is.numeric(genomdat)) stop("genomdat must be numeric") if (!is.numeric(maploc)) stop("maploc must be numeric") data.type <- match.arg(data.type) ina <- (!is.na(chrom) &amp...length(sampleid) != ncol(genomdat)) { warning("length(sampleid) and ncol(genomdat) differ, names ignored\n") …

DNAcopy

updated 5.1 years ago • El

weightCol="V5") Error in .normarg_shift_or_weight(weight, "weight", x) : 'weight' must be a numeric vector, a single string, or a list-like object When I checked the file for the fifth column, it is numeric as followed

ChIPseeker software error

updated 6.8 years ago • vasudha.sharma

cnames[2])</pre> I am very puzzled why `` procset ```` () `` requires exactly one column name. This totally doesn't make sense. In addition, it is very slow for my dataset (19000 single cells). I would like to improve speed...78). For that, I need to know why `` procset ```` () `` requires exactly one column name and whether I can remove this condition. …

ArrayExpress

updated 7.8 years ago • klv2706w

name is deprecated) read_maq_map.cc:150: error: there are no arguments to 'new_XStringSet_from_RoSeqs' that depend on a template...parameter, so a declaration of 'new_XStringSet_from_RoSeqs' must be available read_maq_map.cc:151: error: there are no arguments to 'new_RoSeqs_from_CharAEAE' that depend on a template...parameter, so a declaration of 'new_RoSeqs_from_CharAEAE' must be available read_…

ShortRead Rsamtools ShortRead Rsamtools

updated 15.2 years ago • Bernt Guldbrandtsen

Dear experts, Given the accession IDs such as these: How can I extract the "chromosome name", "start" and "end" position of each ID, with BioConductor. AB002292 AB002296 AB002298 AB002303 .. EF565109 K03493 L36149 M16404

updated 17.3 years ago • Gundala Viswanath

was wondering whether they should be dumped? seqnames strand cigar qwidth start end > <rle> <rle> <character> <integer> <integer> <integer> > SRR031714.2658602 chr2R + 21M384N16M 37 6983850 6984270 ## 2nd mate/read2 > ... > SRR031714.2658602...etc. Therefore I cannot agree your package dumps those alignments. It needs better functio…

Alignment Alignment

updated 11.9 years ago • yun YAN

genome. It seems like bigwig saved with the official NCBI/Ensembl/flybase mitochorion chromosome name dmel_mitochondrion_genome breaks the importation of a previously saved files (which does not break when loaded in...other tools like the Broad IGV). Changing the chromosome name to something smaller fixes the issues. Is that a bug or its per design Look like a bug to me Heres a sample script …

Coverage Annotation rtracklayer Coverage Annotation rtracklayer

updated 11.6 years ago • Marco Blanchette

<div class="preformatted">Dear Mike (and other DESeq2 developers/users), I came across this thread regarding the use of the GLM functions in DESeq2 with respect to time series. However, if I try and perform the analysis you describe then I get an error when estimating the dispersions? do you know what is the cause and/or what I could be doing wrong? dds <- DESeqDataSetFromMatrix( c…

edgeR DESeq DESeq2 edgeR DESeq DESeq2

updated 11.9 years ago • Hickman, R.J. Richard

I would like to make a transcript-based annotation file (TxDb) for Arabidopsis, based on the recent Araport11 genome release. I am using the gff3 file (Araport11\_GFF3\_genes\_transposons.201606.gff, 22 June 2016), available from [here](http://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FAraport11_genome_release). However, this fails because of an error: `` Error …

genomicfeatures txdb makeTxDbFromGRanges

updated 9.5 years ago • Guido Hooiveld

Hello, I want to add gene names to rlog transformation for heatmap, I'm trying to install Biomart but I have some problems with. So I'm asking for another

deseq2 annotation

updated 6.7 years ago • saida3112

tried to create count matrix I used "summarizeOverlaps" of "GenomicAlignments". I always sort BAM by name before this step. But I am now wondering if it's necessary as I haven't see any instruction on this part. I did ask the similar

genomicalignments deseq2 rnaseq

updated 10.5 years ago • Xiaokuan Wei

cg00446235" "cg00563845" "cg00955230" How do I convert these ID's into the standard gene names/symbols in R? Thanks

gene names methylation illumina convertids

updated 7.6 years ago • arbet003

col.histogram = "darkblue", fill.histogram = "darkblue", ylim = c(-.5, 4), name = "Conservation") I receive the following error: Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) : when 'new2old...is NULL, the first elements in the supplied 'seqlevels' must be identical to 'seqlevels(x)' > traceback() 9: stop("when '…

updated 12.7 years ago • Guest User

but I'm having problems, i'm getting this error message: Error in apply(dat, 2, mode) : dim(X) must have a positive length The files that I'm using to test are: sample_info_file: Array name Sample Name Batch array1 sample1_cy3

updated 12.9 years ago • Edwin

be great\]:   1) providing a Data package (let's call it MTseekerData, because that's its name) holding data structures where 2) the S4 class data structures are generated from a package (let's call it MTseeker, because...that's its name), and  3) the package (MTseeker) requires the MTseekerData package and the latter must be submitted as a GitHub issue

developers bioc-devel package development circular dependencies

updated 7.2 years ago • Tim Triche

with: In file included from /usr/lib/gcc/x86_64-redhat- linux/3.4.6/../../../../include/c++/3.4.6/vector:67, from half_range_mode.cpp:4: /usr/lib/gcc/x86_64-redhat- linux/3.4.6/../../../../include/c++/3.4.6/bits/stl_algobase.h:64:28: bits...In file included from /usr/lib/gcc/x86_64-redhat- linux/3.4.6/../../../../include/c++/3.4.6/vector:68, from half_range_mo…

genefilter genefilter

updated 18.8 years ago • Benilton Carvalho

Hi, I am trying to convert gene names to enterz ids for further analysis. I am using: BiocManager::install("AnnotationHub") library(AnnotationHub) hub <- AnnotationHub

Bioconductor

updated 3.1 years ago • gk13102603

It looks fine until the step > dds <- DESeq(dds) estimating size factors Error in .Call(.NAME, ..., PACKAGE = PACKAGE) : Incorrect number of arguments (6), expecting 4 for 'select_hits'. A while ago, I ran another DESeq2 script

DESeq2 Errors

updated 6.8 years ago • joy@wh

GeneRegionTrack", rstarts="exonStarts", rends="exonEnds", gene="name", symbol="name2", transcript="name", strand="strand", fill="#048edd", stacking="squish", name="RefSeq", col="#000000", col.line= "#000000", fontcolor.group...type = "h", col="#0000ff", …

software error Gviz chipseq rnaseq

updated 9.3 years ago • ta_awwad

is missing Error in gene.location$ensembl_gene_id :    $ operator is invalid for atomic vectors > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.5 (El

tcgabiolinks

updated 8.7 years ago • tangming2005

min.sz=10, max.sz=500, verbose=TRUE)$es.obs Mapping identifiers between gene sets and feature names | | 0%) The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec(). Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATI...to debug. ....etcetcetc. The process hangs here. I get the same messages with my own data. I must have overloo…

PROcess GSVA PROcess GSVA

updated 13.0 years ago • David Iles

Hi, I have 5 samples, namely the following: (1) Not transfected, untreated (2) Transfected but untreated (3) Transfected, treated, analyzed after 5 mins...60 mins (5) Transfected, treated, analyzed after 4 hrs [By transfected I mean a particular vector is present, and treated means treated with an antibody] I do not have any replicates for any of the conditions. **I am loo…

edger anova gene expression Dispersion

updated 6.5 years ago • ilovesuperheroes1993

Hello guys! I've been trying to run a DESeq on my RNA seq data, however, when I read in my data and try to run a "DESeqDataSetFromMatrix" the following error pops up. I could really use some help. ```r #read in counts data counts_data <- read.csv('forDESeq2.csv') #for some reason I have gene name duplicates, this eliminates it rownames(counts_data) <- make.names(counts_d…

DESeq2

updated 12 months ago • Kucsera

object has multiple ALTs for a single VCF record, the expanded VCF object seems simply duplicate row names and consequently the row names don't match genetic variations. The following code reproduces this problem (the input...gt; |     <factor> <DNAStringSet> <DNAStringSetList> <numeric> <character> &n…

variantannotation vcf

updated 11.2 years ago • bicycle1885

the same levels as the RleList to force the lists to >>> have the same names as >>> each other: >>> seqlevels(myRegions)<- names(myRleList) >>> viewMeans(Views( myRleList, as(myRegions...IntegerList/NumericList. Same with >> min, max,…

RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge

updated 11.8 years ago • Michael Lawrence

to complete on my data. My data is located in my dirs$data directory (defined below) and has a file named "betas.txt" and "sample\_annotation.txt". Betas.txt has rownames (probe names) as the first column, and sample IDs as the...arguments   My traceback is pasted below, with "..." in between very long seqnames and strand character vectors:   DataFrame(..., check.names = FAL…

rnbeads software error

updated 10.1 years ago • areyoujokingme

fdef, mtable) : unable to find an inherited method for function "gwSnpTests", for signature "character", "smlSet", "missing", "missing" My first question is, why is the 'gwSnpTests' not working? My second question is, do I have to...analyse more than this one chromosome if I wanted to???Is this possible?? It seems as the snp.matrix must be in the form of a list, so maybe I have to create a li…

SNP GO SNP GO

updated 14.1 years ago • Guest User

Aedin: I am using the heatplot in made4, and want to output the re-ordered gene list and column names on heatplot map. Do you know any commands to do it? Xiang </div

made4 made4

updated 15.9 years ago • xiangxue Guo

classes, fdef, mtable) : unable to find an inherited method for function ‘select’ for signature ‘"character"’ I originally thought that this may be due to namespace errors with the package 'ChIPseeker', have tried restarting

AnnotationDbi

updated 5.4 years ago • hina.abbas.bandukwala

conditions. My first issue is that I would really like the transcript IDs to be replaced by the Gene names. I've used Biomart before to convert the transcript ID to ensmbl gene names in the past. But when I do this, I end up with multiple

DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps

updated 3.3 years ago • uhlkatie

Dear user, I trying to read the intensity by the readillumina package. But there is alway error : "Error in analyseDirectory... Directory does not exist". I am not sure why. I refer to other user have sample problem like me ( https://support.bioconductor.org/p/95307/) but the code of the package was similar with his solution. I am not sure why dose it still happen? Is it required that the Sent…

readIllumina

updated 4.0 years ago • Đạt

fetch/52447’ retrieving 2 resources Error: failed to load 'AnnotationHub' resource   name: AH47004   title: clinvar.vcf.gz from dbSNP, GRCh37 assembly   reason: 2 resources failed to download In addition...messages: 1: In curl::curl_fetch_disk(url, x$path, handle = handle) :   progress callback must return boolean</pre> With the error message rep…

annotationhub annotation error

updated 10.0 years ago • elhananby

Error in makeContrasts(diff = "Non neoplastic - Tumor", levels = design.mat) : The levels must by syntactically valid names in R

RNASeqR

updated 4.8 years ago • Rishav

cdsBy(txdb, by=„tx).  In the end I want to obtain a GrangesList object with transcript id as names, and start of startcodon and stop of startcodon (+3 nts), which I then can put in the summarizeOverlaps to count features...on strand orientation), and then built a new GRangesList object.  However, as I know R there must be an easier way to proceed. biomaRt from what I saw does …

biomart bioconductor grangeslist cds ribosome profiling

updated 8.6 years ago • Walter F. Baumann

of chromosome column. Except for the common 22 pairs of chromosome and X, Y, some other chromosome names are strange to me like CHR\_HSCHR17\_2\_CTG5, MT, CHR\_HSCHR8\_3\_CTG1, CHR\_HSCHR7\_3\_CTG4\_4... Could you please

homo sapiens chromosome

updated 7.6 years ago • xchen8