Bioconductor Forum

Hi All, I was wondering if anyone knew a way to get both the intersect and difference of a grange object while expanding out metadata columns. In other words if I had a grange object like this: `` gr1 <- GRanges(seqnames=c(1), ranges=IRanges(start=c(1), end=c(5)), strand=c("*"), mcols=c("a")) `` <code>GRanges object with 1 range and 1 metadata column:<br/>   &nb…

genomicranges intersect

updated 9.6 years ago • zlskidmore

Dear all, I'm using TxDb packages to annotate certain genomic loci to genes. While inspecting my results, I found that a lot of my loci mapped to the same genes. This was suspicious, as their coordinates were very separated, so I inspected the TxDb from which I got the gene information. To get the coordinates of genes in mm10 I'm using the TxDb like so: > library(TxDb.Mmusculus.U…

annotation txdb AnnotationData Genetics

updated 5.6 years ago • Papyrus

or summer students will be available based on interest. Qualifications: Candidates must have completed or will soon complete a Ph.D. or equivalent degree with an emphasis in Bioinformatics, Biostatistics...nih.gov) To Apply: Please send a cover letter, curriculum vitae including bibliography, and the names/contact information of three references to jiyeon.choi2@nih.gov. This position i…

GWAS lung cancer functional genomics eQTL sequencing Job

updated 5.8 years ago • jiyeon.choi2

I/opt/Modules/bzip2/1.0.6/include -I/opt/Modules/zlib/1.2.11/include   -fpic  -g -O2 -c character\_matrix.cpp -o character\_matrix.o g++ -std=gnu++0x -I/opt/Modules/R/3.4.1/lib64/R/include -DNDEBUG  -I"/home/jun.xu/R...I/opt/Modules/bzip2/1.0.6/include -I/opt/Modules/zlib/1.2.11/include   -fpic  -g -O2 -c character\_output.cpp -o character\_output.o …

beachmat scater

updated 8.0 years ago • j.xu3

gt; combineNodes(as.character(1:5), g, "1") Error in graph:::.normalizeEdges(from, to) : 'from' must be length 1 or 1 for this call. > > combineNodes(c("1","2"), g, "X") Error in graph:::.normalizeEdges(from, to) : 'from' must be length 1 or 1 for

graph graph

updated 16.8 years ago • Michael Hahsler

am wrong). Regards, Nik # Experiment with estimating an arbitrary contrast by providing L vector for L'beta. countOfFeatures = 100 countOfSamples = 12 meanResponse = 100 # variance is mu + mu^2/size setSize = 2 set.seed(314...conditionC' # Error in checkContrast(contrast, resNames) : # numeric contrast vector should have one element for every…

deseq2

updated 6.1 years ago • Nik Tuzov

returns all the matches in a Hits object. countMatches(x, table): Returns an integer vector of the length of ?x?, containing the number of matches in ?table? for each element in ?x?. countMatches() is what you can use to...and countMatches() also work on IRanges and DNAStringSet objects, as well as on ordinary atomic vectors: library(hgu95av2probe) library(Biostr…

Cancer IRanges Cancer IRanges

updated 13.0 years ago • Hervé Pagès

<div class="preformatted">On linux you must also change the directory where the file is to 777. This is not very nice because everybody can damage the library. Any hints...div class="preformatted">On linux you must also change the directory where the file is to 777. This is not very nice because everybody can damage the library. Any

updated 20.8 years ago • rue

Error in do.call(rbind, tapply(as.character(groupPathways\[, genecol\]),  : second argument must be a list

mirnapath

updated 8.7 years ago • megha.lal

table(duplicated(markersMatrix$Probe.Name))) ## FALSE ## 1831227 # ... with different names! # Removed duplicates markersMatrix <- markersMatrix[-which(duplicated(markerID)),] # Filter markersMatrix for common

memory problem gaia

updated 8.1 years ago • drusmanbashir

  hi all I am using the RDAVIDWebService to retrieve GO annotation for several gene lists. I was able to run it properly a few day ago but since yesterday I get the following error: <pre> [INFO] Unable to sendViaPost to url[http://david.abcc.ncifcrf.gov/webservice/services/DAVIDWebService.DAVIDWebServiceHttpSoap12Endpoint/] java.net.SocketTimeoutException: Read timed …

software error david rdavidwebservice

updated 10.4 years ago • TriS

something about the data. you will need to learn some R. 1) no embedded blanks in variable (column) names 2) embedded underscores are translated to ".", 3) read.table is powerful and will distinguish between numeric and character

hgu95av2 Biobase affy limma hgu95av2 Biobase affy limma

updated 22.3 years ago • Vincent J. Carey, Jr.

<div class="preformatted">Dear All, Sorry to bother those who are not interested. We have 2 open positions at Sophia Genetics (http://www.sophiagenetics.com) If you are interested, please contact Dr Zhenyu Xu (zxu at sophiagenetics.com). The deadline for the application is 31st Aug 2013. best, zhenyu About the company: Sophia Genetics SA helps clinical laboratories that perform…

Genetics Alignment Visualization Genetics Alignment Visualization

updated 12.5 years ago • Zhenyu Xu

than "gMDSC from ascites". Here's a (not complete) exemple of my annotation df, with sample names as rownames. cell_type cond origin group CA.gMDSC.Blood gMDSC Cancer_Blood 1 gMDSC_Cancer_Blood DE.gMDSC.Ascites...A03.gMDSC gMDSC Ascites 2 gMDSC_Ascites With…

deseq2 annotation normalization

updated 5.8 years ago • christophe.vanhaver

and prepare package for lazy loading Error in buildLookupTable(letter_byte_vals, codes) : 'vals' must be a vector of the length of 'keys' Error: unable to load R code in package 'Biostrings' Installation halted ERROR: lazy loading

Biostrings packageinstallation

updated 16 months ago • semra

<div class="preformatted">Hello I have issues in getting RCytoscape to recognize edge attributes. What I am doing wrong? Thanks! -burak rlNt();runNt("send2RCy") entering RCytoscape::displayGraph sending 11 nodes sending 22 edges adding node attributes... [1] "label" [1] "moleculeType" adding edge attributes... [1] "weight" Error! RCytoscape::setEdgeAttributes, attributes not initialized.…

graph RCytoscape graph RCytoscape

updated 13.9 years ago • Burak Kutlu

type="UNIPROT_ACCESSION", annot=NULL, tool="geneReport") Error in strsplit(string, "<!--") : non-character argument </pre> </td> </tr> <tr> <td> </td> </tr> <tr> <td> </td> </tr> </tbody> </table

DAVIDQuery

updated 10.5 years ago • manejferreira

<div class="preformatted">I have 2 vector ,such as a=1,2,4,5,6,8 b=2,5,8,9,6,4 . how to calculate the mutual information of a and b in bioconductor .Is there any package or function...div class="preformatted">I have 2 vector ,such as a=1,2,4,5,6,8 b=2,5,8,9,6,4 . how to calculate the mutual information of a and b in bioconductor .Is there any package or

updated 17.6 years ago • jiabao xu

mc.cores=2) [[1]] [1] "Error in as.list.default(X) : \n no method for coercing this S4 class to a vector\n" [[2]] [1] "Error in as.list.default(X) : \n no method for coercing this S4 class to a vector\n" > sessionInfo() R version 2.13.0 Under

GenomicRanges GenomicRanges

updated 15.0 years ago • arne.mueller@novartis.com

packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf>, I understand that I have to create 2 vectors, one with all my genes, and other with the DEGs. After that, I get lost. What I have done until now in order to create the vectors

goseq DESEQ2 RSTUDIO CODE

updated 10.2 years ago • amyfm

If I try to create a Euclidean distance object it crashes out with a memory error ( > Error in vector("double", length) : vector size specified is too large ). This seems strange as I have 3GB ram, which I would think is plenty. Any

Clustering Cancer Clustering Cancer

updated 18.9 years ago • Daniel Brewer

which is giving me a bit of a headache. I read somewhere that it may be due to illegal ALT character but it does not appear to be the case. > ref <- FaFile("sequences.fa") > coding <- predictCoding(vcf, txdb, seqSource...nbsp;     19.5:3:10:5:0   0/0:0.0,-2.11,-35.4:5:21:10:0  By the way there must be an easier way to recover S…

variantannotation predict coding

updated 10.8 years ago • Miss Agnieszka Aleksandra Golicz

<div class="preformatted"> Dear Bioconductors, I am struggling with the creation of an annotation package and the namespace involved. I apologize if this is a trivial question, but I am not very familiar with namespace issues. I created environments containing annotation data using functions I wrote for that purpose (for some reasons I do not want to use AnnBuilder). This did work, since …

Annotation Annotation

updated 17.9 years ago • Georg Otto

featuretype <Rle> <IRanges> <Rle> | <CharacterList> <character> <character> 1 [ 335, 649] + | YAL069W YAL069W protein_coding 1 [ 538, 792] + | YAL068W-A YAL068W-A protein_coding 1 [ 2480

granges txdb genomicfeatures

updated 9.9 years ago • vinod.acear

div class="preformatted">Greetings, I must have been blind. where could I find getBioC() function? in reposTools package? I could not find it there. thanks -hui [[alternate

updated 22.9 years ago • Wang, Hui

gt; pathways <- try(get.pathways.by.compounds(c("cpd:C00033", "cpd:C00328"))) > pathways > #character(0) #does not work# > pathways <- try(get.pathways.by.compounds("cpd:C00328")) > pathways > #character(0) #does not work...cpd:C00033")) Actually get.pathways.by.compounds(c("cpd:C00033", "cpd:C00328")) should return character(0). I tried it via a j…

Pathways KEGGSOAP Pathways KEGGSOAP

updated 19.2 years ago • Nianhua Li

arrqy1.samples" not found > array1.samples Object of class marrayInfo. maLabels # of slide Names experiment Cy3 experiment Cy5 date comments 1 1 1 array1.1.spot wildtype ref 10/31/2003 NA 2 2 2 array1.2.spot wildtype...is not a multiple of the number of columns 2: number of rows of result is not a multiple of v…

Transcription Cancer Transcription Cancer

updated 22.2 years ago • Richard Friedman

Hi all, I am trying to use Limma for proteomic analysis on a sample size of n=8 controls and n=8 experimental. The code runs without errors, but the results show that nearly all 700 proteins are significant and the p-values are tiny (ex. 3.02e-10). I feel like something must be wrong with the data preprocessing because these results don't seem right. Also, the resulting volcano plot has a li…

Proteomics limma

updated 20 months ago • Abbey

1:10], Hsapiens, upstream=300, downstream=0) Error in .getOneSeqFromBSgenomeMultipleSequences(x, name, start, NA, width, : sequence chr19 not found In addition: Warning message: In .Seqinfo.mergexy(x, y) : The 2 combined objects have...sequence levels in common. (Use suppressWarnings() to suppress this warning.) # Change chromosome naming style: > seqlevelsStyle(Hsapiens) = "U…

bsgenome genomeinfodb transcriptdb

updated 11.1 years ago • Diego Diez

I have checked whether the files exist, and all files do. All these files have a long "transcript name" but I'm already using the appropriate data frame to map them to the gene ids. However, I get a `rowsum` error, saying something...counts summarizing length Error in rowsum.default(x[sub.idx, , drop = FALSE], geneId) : 'x' must be numeric ``` I tried importing the same files with `m…

tximport

updated 4.9 years ago • Ezgi

anyway to specify the genome build to get hg19 chromosome position? ```r snp_ids=scan(infile, character(), quote="") snp_mart = useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp") snp_attributes = c("refsnp_id", "chr_name", "chrom_start

biomaRt biom

updated 4.2 years ago • lei.shang

I can't seem to post a question - it just fills with red. I made sure there are not unusual characters (at least in the text bits) but I can't get this to work. ![enter image description here][1] and ![enter image description

Bioconductor

updated 23 months ago • DS

From BiocCheck : * NOTE: Consider shorter lines; 501 lines (14%) are > 80 characters long. Most of these lines are roxygen comments. formatR package says : > Also note that single lines of long comments

BiocCheck

updated 4.3 years ago • ZheFrench

not return any results indicating that is not available.  __BiocManager::available("biocValid") character(0)__ Many thanks for your help. &nbsp

biocmanager

updated 7.1 years ago • mariatuffy

Gordon PS. I haven't included you original post in my reply because there were so many non-standard characters imbedded in it. ______________________________________________________________________ The information

updated 11.5 years ago • Gordon Smyth

For `dominance` function, > `x`: A species abundance vector, or matrix with the absolute count data (**no relative abundances**). This seems intended for 16S data analysis. How can a...For `dominance` function, > `x`: A species abundance vector, or matrix with the absolute count data (**no relative abundances**). This seems intended for 16S data analysis. How can a user

microbiome

updated 21 months ago • Dario Strbenac

hits: package or namespace load failed for ‘org.Hs.eg.db’: $ operator is invalid for atomic vectors Thank you in advance for your time and suggestions

org.Hs.eg.db

updated 4.7 years ago • Chloe

values in a matrix. if I have 3 in log2 => 2^3=8 in decimal, how I do that in R for an entire vector or matrix? Thanks </div

updated 18.6 years ago • D.Enrique ESCOBAR ESPINOZA

for 'org.Hs.eg.db', details: Call: l$contains Error: $ operator is invalid for atomic vectors

org.Hs.eg.db

updated 4.7 years ago • Chen

in R using the View() function. __> View(Golub\_Merge) __ and, I get this error: __Error: VECTOR ELT() can only be applied to a 'list', not a 'builtin'__ Please help

golubEsets rstudio

updated 9.9 years ago • shramanathakur

Hi there, I am using QDNAseq to call CNA in sWGS data. Initial results showed CNAs in centromeres areas of several chromosomes, recurrently in all samples (benign and tumor samples). I am trying to mask centromeres and telomeres, following the instructions: ```r bins$blacklist = calculateBlacklist(bins, bedFiles = c("hg38blacklist.v2.bed", "centromeres_region_hg38.bed", "GAPlocations_hg38.bed…

QDNAseq blacklist CopyNumberVariation blocklist

updated 4.1 years ago • briverog

The error i'm getting is ``` Error in order(genes$Start, genes$End) : argument 1 is not a vector ``` I think the issue is with line 17 of the `plotExonJunc` function, it tries to order the genes by `order(genes$Start, genes...rep(75605, 250), rep(75033, 250)) # make fit using voom, voom 'design' defaults to unit vector v <- voom(dge) fit <- lmFit…

limma

updated 6.3 years ago • dleng

<div class="preformatted">hello all, I know problems regarding memory allocation has been asked a number of times and i followed those solutions too but still i am not able to resolve this issue.... > fns2=list.celfiles(path="C:/Program Files/R/R-2.10.1/koolfile",full.names=TRUE) > rawdata=ReadAffy(filenames=fns2) Error: cannot allocate vector of size 640.9 Mb > m…

updated 15.8 years ago • sneha patil

Ctrl), where I provide either x, y or z TFs individually, or simultaneously using a multicistronic vector (xyz); Ctrl represents a control vector infection. Each group has 5 replicates. Data has been filtered for 0 counts removal

deseq2 contrast

updated 8.9 years ago • sebastiano.curreli

files into a BamFileList with the same samples as listed in the .csv list=BamFileList(path, index=character()) library(GenomicFeatures) \#Obtain Reference genome from UCSC  Txdb=makeTxDbFromUCSC(   genome="hg19", &nbsp...groups res<-results(dds, contrast=c("group", "HF2303.Control", "HF2303.TMZ")) \#Match Gene Names to the Ensembl IDs from the …

deseq2 results rstudio

updated 10.5 years ago • Lillyhchen

<div class="preformatted"> Hello, I have qPCR data that does not have Well and Plate info to populate qPCRBatch object. As your vignette points, out, I am trying to create an eSet object: > frame<-read.delim("dreamy.csv", skip=2, sep="\t", colClasses="character") > n=30 > head(frame) Actin_022.Triton.X.control.hskg.20.59.1 1 Actin_022\tTriton-X\tcontrol\thskg…

qPCR Annotation HTqPCR qPCR Annotation HTqPCR

updated 12.9 years ago • Guest User

in if (is.null(nms) && 0L != ncol(assays[[1]])) stop("'SummarizedExperiment' assay colnames must not be NULL") : missing value where TRUE/FALSE needed</pre> It seems to me my pData, fData are fine for my eSet data as: <pre> > barley.eset...ExpressionSet (storageMode: lockedEnvironment) assayData: 47748 features, 15 samples element names: exprs protoco…

software error summarizedexperiment

updated 9.8 years ago • yifangt

preformatted">Hi, when I read the cel files bioconductor gives me warning "Error: cannot allocate vector of size 86400 Kb". How can I fix the problem? Your help is greatly appreciated. Lang Chen</div

updated 22.8 years ago • Lang Chen

the code in the working paper "Differential expression with bioconductor project". I obtain a null vector when use the instruction: esetSub$mol=="BCR/ABL" is it correct? Thanks in advance! </div

updated 20.3 years ago • fede@dssm.unipa.it

but I got this error: > Error in .local(con, format, text, ...) : negative length vectors > are not allowed Can you help me? Thank you

rtracklayer

updated 6.5 years ago • ribioinfo

option is 0.05,1e+07.  Does this mean that if entire chromosome arms are lost, they must not total more than 5% of the genome?   &nbsp

Purecn maxhomozygousloss

updated 7.1 years ago • twtoal

PRECEDEID FOLLOWID <rle> <iranges> <rle> | <factor> <integer> <integer> <integer> <character> <integerlist> <character> <characterlist> <characterlist> [1] chr1 3204352 - | intron 137755 137755 1 228337 6510 [2] …

VariantAnnotation vari

updated 10 months ago • Marco

<div class="preformatted">Dear BioCs, I'm trying to create a heat plot with a matrix containing real time PCR data for just 5 genes. There are 105 samples, belonging to 7 groups (groups are in numerical order). The matrix looks like this (Age is my grouping variable): Gene1 Gene2 Gene3 Gene4 Gene5 Age A1R_D03 -13.71434 -14.19288 -15.79439 -14…

graph graph

updated 17.5 years ago • Amy Mikhail

gt; cds CountDataSet (storageMode: environment) assayData: 12063 features, 12 samples ? element names: counts protocolData: none phenoData ? sampleNames: 2713:InfAF 2700:InfAF ... 2684:Cont (12 total) ? varLabels: sizeFactor group...sapply(tapply((1:ncol(counts))[replicated_sample], factor(conditions[replicated_sample]),? : ? 'x' must be an array of at least two dimensions I can't reproduce this…

GO edgeR DESeq GO edgeR DESeq

updated 14.0 years ago • Iain Gallagher

Hi, I am trying to use fastMNN for integrating snRNA-seq data from different samples of tissue at progressive stages of development. Some of the samples are biological replicates. Two samples are run together in one sequencing run, but they are not necessarily the same time-point or same individual. While reading the mnncorrect paper, I realized that he authors have made a note that each dat…

scrna-seq integration batch correction

updated 6.0 years ago • p.joshi

<div class="preformatted">Hello, I am getting no matches using locateVariants, while I would expect some. Here is one example: gr= GRanges(seqnames=Rle('chr12'), ranges= IRanges(33804059, 33804059)) txdb= TxDb.Mmusculus.UCSC.mm9.knownGene length(locateVariants(query= gr, subject= txdb, region=AllVariants())) [1] 0 Warning message: In `start<-`(`*tmp*`, value = c(4795974L, 4795974L,…

updated 12.1 years ago • mattia pelizzola

mixes with statistics. I come from the Machine Learning field, and usually have problems with the naming conventions (well, among several other things, I must admit). Besides, I am not an expert in statistics, having used the barely

probe ASSIGN probe ASSIGN

updated 13.6 years ago • Gustavo Fernández Bayón

read.maimages() will already contain annotation information from the Agilent output files. Look at names(RG$genes) to see what you have. Secondly, does your GAL file match your data files? Type dim(RG) and gal <- readGAL() dim(gal) Do...on each array as a technical >replicate, but since the spacing is not consistent for each gene, I must >first order th…

limma limma

updated 18.8 years ago • Gordon Smyth

the genomic positions on a particular chromosome, on the Y axis the coverage of SNPs. Besides the vectors containing the position and the coverage, I have a vector for the color of each point (color\_point : eg all are "grey" and...1 in particular is "red"), and a vector for the size of each point (size\_point : eg all are "1" and 1 in particular is "5"). When I create the datatrack to show the …

gviz

updated 7.8 years ago • cedric.vmdl

dataset. I am encountering the following message: *Error in seq_len(length(idx) - 1) : argument must be coercible to non-negative integer* and cannot proceed with my analysis. P.s. see details of my script below. Any suggestions...analysis pipeline for mouse and Drosophila datasets without any issues. A check for duplicated row names indicates 418. Is this a formatting issue and how do i reso…

Celegans DESeq2 dds Errorinseq_len(length(idx)-1)

updated 3.2 years ago • Enzo.Scifo