Bioconductor Forum

on google or on the bioconductor and R web sites. I have two CEL files and one CDF file. The name of the cdf file is L_monocyto530090.cdf. I am using makecdfenv to make a package out of it. I have found out that the CDF...name seems to be specified in the CEL files, and in these files it is stated as L_monocyto530090.1sq. I have seen that bioconductor...strips all non-letter/number characters fr…

cdf makecdfenv cdf makecdfenv

updated 20.6 years ago • Karin Lagesen

Hi all, I am receiving this error message when running MAI to impute missing values: ```r gp.mai <- MAI(gp.raw, MCAR_algorithm="BPCA", MNAR_algorithm="Single", assay_ix=1) Estimating pattern of missingness Imposing missingness Generating features Training Error in randomForest.default(x, y, mtry = min(param$mtry, ncol(x)), ...) : long vectors (argument 28) are not supported…

randomForest MAI

updated 3.4 years ago • Hans-Ulrich Klein

<div class="preformatted">Dear all, I have some problems with the error "cannot allocate vector of size..." I am using the Bioc package "arrayQualityMetrics" to assess the quality of a microarray experiment saved in an Affybatch object (rawData) but I encountered the same problem with oneChannelGUI package, when I apply the gcrma function. My pc has 3.37 GB RAM. I read several posts in the …

Microarray gcrma Microarray gcrma

updated 13.9 years ago • Manuela Di Russo

I am adding gene names to my results from DESeq2 however, I am running into a problem and don't know how to fix it I am getting the hgnc_symblo...I am adding gene names to my results from DESeq2 however, I am running into a problem and don't know how to fix it I am getting the hgnc_symblo column...padj ensembl entrez <numeric> <numer…

biomaRt gene annotation

updated 5.8 years ago • jnaviapelaez

gt; 0 & Student.s.T.test.q.value < 0.005), quannumber=6, logfold=T)` Then, I create a vector of background genes from the original data frame `foldGO_background_genes <- minimal_GOfiltered[,1]` and retrieved...GO DAG topology .......... ( 0 GO terms and 0 relations. ) Nothing to do: Error in split.default(names(sort(nl)), f.index) : first argument must be a …

FoldGO GSEA

updated 5.1 years ago • lessismore

Hi, I\`m trying to use DiffBind package and having an error with __dba__ command: cannot allocate vector of size 2GB. I\`m running the most recent DiffBind version, 64-bit version of R on a computer with 8GB RAM. I reduced the number

R diffbind

updated 8.3 years ago • ekgush

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updated 18.6 years ago • Maurice Melancon

instead of the gmt file included in the package, but I get `` `Error in FUN(X[[i]], ...) : index must be either integer vector` `` in R. I tried to ways of importing the gmt file as below, none were successful. <code>`gmt <- Sys.glob

R BioQC gmt GSEA

updated 8.2 years ago • Seymoo

space ranges | strand transcript <factor> <iranges> | <integer> <character> 1 chr1 [301409811, 301409969] | -1 AC185612.3_FGT006 2 chr1 [301362751, 301363304] | -1 GRMZM5G884466_T03 3 chr1 [301353831...301353260] | -1 GRMZM5G884466_T03 gene exon biotype <character&…

Sequencing RNASeq edgeR easyRNASeq Sequencing RNASeq edgeR easyRNASeq

updated 12.3 years ago • Guest User

get an error message from limma2annaffy() function. Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs I get the annotated HTML and txt tables for each desired contrast by using...you want to accept or change these values? [ a/c ] a Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs ## gene numbers …

GO GUI annaffy oligo oligoClasses KEGGREST GO GUI annaffy oligo oligoClasses KEGGREST

updated 12.0 years ago • Guest User

Apologies for what I expect will be an easy solve. I have built an Expression Set from scratch using the instructions at http://www.bioconductor.org/packages/2.13/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf I have the expression set imported as a matrix, the pheno Data imported as a data.frame from a cvs file. Biobase readily creates a 'formal class ExpressionSet',…

pvca biobase

updated 10.4 years ago • a.riedel

R source, and vignette source... * NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters long.</pre> I have all the files mentioned and of course, I'm going to try one more time... I feel sure others have grappled

bioccheck package development

updated 8.2 years ago • Paul Brennan

Dear goseq developers：       Hello ,my name is Xu,ZhengZheng ,a student of Beijing Institute of Gennomics ,Chinese Academics of Science. After I use edgeR to do difference...Question2:when I use goseq(pwf,"hg38","refGene"),it pop-up code with errors:   ___in names(tmp) = rep(names(map),times=as.numeric(summary(map)\[,:attempt to set an attri…

goseq

updated 10.4 years ago • xdzperfect

rd1 RangedData with 3 rows and 1 value column across 2 spaces space ranges | score <character> <iranges> | <numeric> 1 chrA [11, 20] | 5 2 chrB [31, 40] | 10 3 chrB [51, 60] | 15 ###### filter based on score > rd1filt <- rd1[rd1[["score"]]>= 10,] &gt...RangedData with 2 rows and 1 value…

Cancer Cancer

updated 15.8 years ago • Janet Young

pre> Error in .Call("R_disscosangle", as.vector(X), as.numeric(dim(X)[1]), : negative length vectors are not allowed</pre> I can recreate the error as follows (session info included): <pre> > library("hopach") > test <- matrix...Error in .Call("R_disscosangle", as.vector(X), as.numeric(dim(X)[1]), : negative length vectors are not allowed &…

hopach

updated 10.7 years ago • ejliaw

list, I noticed that GRangesList objects are not allowed to have outer elementMetadata columns with names identical to names of inner elementMetadata columns (see below) Is this restriction necessary? And if yes, should identical...names raise an exception at the time of construction rather than further down the line? Best wishes, Leonard > gr <- GRanges...Error in validObject(…

updated 12.2 years ago • Leonard Goldstein

consideration. library(parallel) lines <- readLines("/usr/local/Rmpi/hostfile.plain") hosts <- character() for (line in lines) { x <- (strsplit(line[[1]], " ")) hosts <- c(hosts, rep.int(x[[1]][1], as.integer(x[[1]][2]))) } #THIS LINE HANGS #HOSTS IS A CHARACTER...VECTORS OF IP ADDRESSES FOR BIOCONDUCTOR AMIs CREATED FROM STACK TEMPLATE cl <- ma…

updated 13.1 years ago • Mortimer, Steven

cannot have `const' method qualifier /usr/include/c++/3.2.3/bits/fpos.h:103: `bool operator==(...)' must have an argument of class or enumerated type /usr/include/c++/3.2.3/bits/fpos.h:103: `bool operator==(...)' must take exactly two arguments...cannot have `const' method qualifier /usr/include/c++/3.2.3/bits/fpos.h:107: `bool operator!=(...)' must have an argument of class or enumerate…

genefilter genefilter

updated 16.2 years ago • Denise Mauldin

quietly = TRUE) >data2<-read.table("Goutput_chr_1.txt",sep='\t',header=TRUE,colClasses =c('character','character','numeric','numeric','numeric', 'numeric')) >head(data2) ID chrom loc.start loc.end num.mark seg.mean 1 G20020876...ID"]),10))),]),by = "gene", imput=FALSE,XY=FALSE,geneMap=geneInfo) Error in match.arg(what) : 'arg' must be of length 1 I am no…

cghMCR cghMCR

updated 10.5 years ago • viritha kaza

file group description Length:4 Length:4 Length:4 Class :character Class :character Class :character Mode :character Mode :character Mode :character > names(targets) [1] "file" "group" "description

edgeR edgeR

updated 13.6 years ago • Guest User

features=ebg, reads=bamfiles, mode="Union", singleEnd=FALSE, ignore.strand=FALSE) Error in names(res) <- nms : 'names' attribute [2] must be the same length as the vector [1] In addition: Warning messages: 1: In serialize(data, node

GenomicAlignments

updated 6.8 years ago • mahmudornob

also lists the gc content % for each chromsome ``` But then when I tried to change the chromosome names... ``` # # Store mapping in R as vector # chr_map <- c( # "1" = "CM021939.1", "2" = "CM021940.1", "3" = "CM021941.1", # "4" = "CM021942.1", "5" = "CM021943.1", "6" = "CM021944.1...match # # length(original_chr_names) == length(new_chr_names) # # # # Assign the new chromosome names #…

BSgenome.Mfascicularis.NCBI.6.0

updated 10 months ago • Genevieve

end=10020) #but then when I use start=full.df$Start. It naturally throws an error saying 'start' must be a vector of integers Questions: How Do I handle this? Does start here mean that each chromosome numbering starts from...1? How do I split each sequence retrieved and create as fasta format (>)with sequence name attached to them retrieved from my input file? >sessionInfo() …

BSgenome BSgenome BSgenome BSgenome

updated 14.4 years ago • viritha kaza

process. However, I encountered the memory problem error message like this: Error: cannot allocate vector of size 594075 Kb I got this error message while I was trying to apply dChip preprocessing procedures for 150 Affymetrix...PM/MM correction : pmonly expression values: liwong normalizing...Error: cannot allocate vector of size 594075 Kb > gc() used (Mb) gc trigger (Mb) …

PROcess trigger PROcess trigger

updated 21.0 years ago • Tae-Hoon Chung

1974 ranges and 2 metadata columns: seqnames ranges strand | name score <rle> <iranges> <rle> | <character> <numeric> [1] chr2 83972890-83972905 + | SRF_MA0083.3 8.61532 [1974] chr4 106237089-106237104...ranges strand | gene_id…

plyranges

updated 6.2 years ago • Aditya

nbsp; its works with out problem   I used targets$FileName the out put all the file name  with information in targets file ? no problem , and i specify the path : x <-read.maimages(targets$FileName,path...Ad2",source="agilent.median"); but i have this error : Error: '\\U' used without hex digits in character string starting ""C:\\U"   :(&am…

limma

updated 10.7 years ago • naving2uk

WashU and they claim the data is directly exported from GenomeStudio. Could it be from unexpected characters in the file (e.g. R doesn't like #, -, and other characters in certain situations)? There aren't any #'s in the file, but I'm curious...is read.ilmn handles these cases. The sample names do have '-' in the name, but I tried removing those and it didn't make a difference. I appreciate you…

Microarray Microarray

updated 13.1 years ago • Mark Ebbert

error *sometimes*: Error in get(name, envir = .classTable) : formal argument "envir" matched by multiple actual arguments The first time, I retrieved the index...ran the loop again, just for fun. This is the code: library(BSgenome.Mmusculus.UCSC.mm8) # create vectors to store results in: newseq2<-vector(mode="character", length=dim(UInfo)[1]) newstart2<-vector(mode="numeric", l…

Microarray Annotation BSgenome BSgenome Microarray Annotation BSgenome BSgenome

updated 15.6 years ago • J.delasHeras@ed.ac.uk

2GB of RAM running kubuntu Gutsy version 7.10, However I've got the same error "can not allocate vector of size 73 kb" as well. I'm not sure whether this is related to the specific function/package that I'm using, since I've got...header=TRUE,row.names="geneNames") > coin <- cia(data1723,data2224) Error: cannot allocate vector of size 73 Kb > > dim(data1723) [1] 9335 …

updated 18.2 years ago • Amin Moghaddasi

div class="preformatted">Hello, I have used the 'names' function in flowViz to place percents of the gated population within the plot. I have never figured out how to get the...plot automatically, but at least I could place the numbers in the plot. With quadrantGate plots the 'names' function does not appear to do anything. Is there a mechanism to access this and label the plot quadrants? Th…

flowViz flowViz

updated 15.3 years ago • Aric Gregson

_Error in new\_Hits(Class, from, to, nLnode, nRnode, mcols) :    'nLnode' and 'nRnode' must be single integers)_ which I am not sure how to resolve.    __distanceToNearest(myRanges1, myRanges2, ignore.strand...Error in new\_Hits(Class, from, to, nLnode, nRnode, mcols) :    'nLnode' and 'nRnode' must be single integers__ __myRanges1__ …

genomicranges DistanceToNearest

updated 9.3 years ago • roladali

to specify the 6 expressions explicitly when calling makeContrasts? I tried to first create a vector with those expressions and use that in makeContrasts: > pair<-c() > ind<-1 > for (i in 2:numg){ + for (j in i:numg) { + pair[ind] &lt...1 GroupB 1 GroupC 0 The help page says: "...: expressions, or character strings which can be…

limma limma

updated 20.6 years ago • He, Yiwen NIH/CIT

Hi. How to convert 'lncRNA probe name (ex. p2966)' or 'mRNA probename (ex. A_19_P00315593)' to gene symbol? I use 'GSE115018' data for practice. To convert probe name to...biomaRt', 'org.Hs.eg.db' and etc. package. Which package should I use to convert probe name into gene symbol

lncRNA probeID mRNA genesymbol

updated 2.9 years ago • Sooni

Dear Utents, I am running fitGAM function using a PseudotimeOrdering object from a single-cell dataset. Dimnames of both datasets are two lists of characters, while different results for dimnames specifying [1]. I attached the results in R below. I ran this code last week and...a PseudotimeOrdering object from a single-cell dataset. Dimnames of both datasets are two lists of characters, wh…

SingleCellExperiment singlecelle scRNAseq

updated 4 months ago • Francesco Silvestro

Hi all, I performed a PCA and I want to group vector (variables) around PCA origins into 5 degrees arc clusters. Any idea on an R code that would do it? Or even any R code that

pca plotpca

updated 9.2 years ago • marianarochadesouza

<div class="preformatted">dear List, Sorry for the silly question, but I am a R beginner and try to sort something out. I have a vector named match containing N positions match=c( "1_880238", "1_883625", "1_1222695", "1_2255524" ,"1_887560") I have a big data frame containing a lot of infos (among those positions in the first column V1 in the same format as in the match vector, example.txt …

updated 14.3 years ago • nac

the topGO package has a serious bug in that the column reporting the results of the test is of type character instead of numeric. Example: ```r library(topGO) data(GOdata) data(results.tGO) sig.tab <- GenTable(GOdata, Fis = resultFisher

GenTable topGO

updated 4.8 years ago • dario.beraldi

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 the GRanges object, everything seems to be in order: <pre

genomicranges

updated 7.4 years ago • bbrink

transcripts_tx_chrom, NA, "transcripts$tx_chrom", : all the values in 'transcripts$tx_chrom' must be present in 'chrominfo$chrom' In addition: Warning message: In .deduceExonRankings(exs, format = "gtf") : Infering Exon Rankings...it worked but the warning reminded me of the "exonRankAttributeName" argument and the chromosome names are now different from the ones in the genome file and there …

Annotation TranscriptDb Annotation TranscriptDb

updated 12.7 years ago • Ugo Borello

con, statement, bind.data) : RS-DBI driver: (RS_SQLite_exec: could not execute: PRIMARY KEY must be unique) In addition: Warning messages: 1: In is.na(v) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(v) : is.na() applied...to non-(list or vector) of type 'NULL' 3: In is.na(v) : is.na() applied to non-(list or vector) of type 'NULL' Timing stopped at: 0.36 0.01 0.44 &…

updated 17.5 years ago • Michael Gormley

column-only format. What if I am looking to extend the profile of the GRanges object by including a character attribute. eg. temp <- GRanges(seqnames= . . . , ranges = . . .) temp$name <- "ABC" Here I want to have a character variable (accessible

genomicranges granges

updated 7.1 years ago • Shaurya Jauhari

T2$sym, "hgu133plus2.db", anncols) Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs So I removed the NA annotated probes with: > T3 <- T2[complete.cases(T2[ , 2:3...T3$sym, "hgu133plus2.db", anncols) Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs …

aafTableAnn microarray annafy hgu133plus2.db

updated 7.0 years ago • maxininfa

readAligned(dirPath=dir,type="MAQMap") > Error: UserArgumentMismatch > 'dirPath', 'pattern' must be 'character(1)' > > I tried specifying the pattern argument but the function still doesn't work. > >> aln <- readAligned...dirPath=dir,pattern="S.*",type="MAQMap") > Error: UserArgumentMismatch > 'dirPath', 'pattern' must be '…

Cancer PROcess ShortRead charm Cancer PROcess ShortRead charm

updated 16.8 years ago • Martin Morgan

<div class="preformatted">Hello everybody, I have a list of over 9000 EntrezID . each lines contains one or probe-IDs as here: > head(probeSetList) $`10` [1] "38912_at" $`100` [1] "41654_at" "907_at" $`1000` [1] "2053_at" "2054_g_at" $`10000` [1] "40781_at" $`10001` [1] "35430_at" "35431_g_at" "35432_at" $`10002` [1] "31366_at" "31667_r_at" I would like to sort this lis…

updated 16.0 years ago • Assa Yeroslaviz

cryptic error messages. After tracking down the problem I found out that this was due to the file names I used. My file names started with numbers and contained "-" signs. In the r3Cseq pipeline the filenames are used to name the...matrices and files that are created. By default R changed the file names by adding X in front of the numbers and replacing "-" by ".". As a result the r3Cseq package …

r3Cseq

updated 10.7 years ago • felix.klein

was used to compute and identify the differentially expressed genes. Now, we have a question about vector backbone: Although we have doing a local background subtraction, how did we control for or remove background hybridization...to the vector backbone? Have you any ideas? All comments/criticisms are very welcome! Thank you very much. -- Marcelo Luiz de Laia Universidade

Normalization limma Normalization limma

updated 17.2 years ago • Marcelo Laia

vocabulary game, Wordle, is [wordle](https://wordleunlimited.one). Letters ranging from four to ten characters in length can be used in Wordle Unlimited's gameplay. Coming up with a new phrase or changing the difficulty level

alabaster.schemas db0

updated 22 months ago • minton

the error: The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. head(cleanDat.editrow[1:5,1:5]) rownames(cleanDat.editrow) dim(cleanDat.editrow) #31391, 532 # mart

biomaRt

updated 6.2 years ago • coyoung

div class="preformatted">HI, Does anybody know how to control the order of the column names displaying in the heatmap (heatplot)? I was trying to compare two heatmaps with same set of genes as row names and same set...of patient samples as column names. The result shows a different order of column names. I want they display in the same order in the heatmap pictures. regards

updated 15.4 years ago • xiangxue Guo

error message: > decideTestsDGE(lrtAll) Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x),  :   'data' must be of a vector type, was 'NULL' > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86

Genetics edgeR

updated 11.3 years ago • Jon Bråte

rgb(225, 226, 229)">Error in as.vector(data) :   no method for coercing this S4 class to a vector</span> I've found similar questions where they explain you have to add __`` importMethodsFrom(S4Vectors,as.matrix) ``__

mclust s4vectors S4 as.matrix .FCS

updated 9.5 years ago • anara92

data.frame, RangedData and GRanges, respectively): > ex1[1,] bin chrom chromStart chromEnd name score strand signalValue pValue qValue 1 3 chr1 150941733 151007265 . 297 . 2.98199 13 -1 > ex2[1,] UCSC track 'wgEncodeBroadHistoneGm12878CtcfStdPk...UCSCData with 1 row and 3 value columns across 93 spaces space ranges | name sco…

BSgenome BSgenome rtracklayer BSgenome BSgenome rtracklayer

updated 13.0 years ago • Gustavo Fernández Bayón

Prepare the 'metadata' data frame ... metadata: OK Now generating chrominfo from available sequence names. No chromosome length information is available. Error in .normargSplicings(splicings, transcripts_tx_id) : 'splicings...cds_start' must be an integer vector In addition: Warning messages: 1: In .deduceExonRankings(exs, format = "gtf") : Infering Exon Rankings. If

TranscriptDb TranscriptDb

updated 12.9 years ago • Fong Chun Chan

found: The basicProfile() function is expecting you to give it a central ID for the org package you name for it. It seems to be assuming that this will be an entrez gene ID. But that is *not* what the arabidopsis community usually...org.At.tair.db, uses TAIR IDs as the central ID (this is why TAIR is in the middle of the package name). You can get and use entrez gene IDs with the org.At.tair.…

GO Organism goProfiles GO Organism goProfiles

updated 12.4 years ago • Marc Carlson

with 454075 ranges and 1 metadata column: > seqnames ranges strand | name > <rle> <iranges> <rle> | <character> > [1] chr10 1-94200 * | 15_Quies > [2] chr10 94201-96600 * | 9_Het > [3] chr10 96601-119…

GenomicRanges

updated 5.7 years ago • Zach Roe

chromosome lengths for BSgenome.Rnorvegicus.UCSC.rn5... Calculating genomic coordinates...Error in vector(length = supersi ze_chr[length(chromosomes)], mode = "character") : vector size cannot be NA/NaN Thank you very much! thanks, Yuting

Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS

updated 12.3 years ago • Guest User

T, sep=",") > tmp <- (DE$padj < pcutoff) > geneList <- tmp > names(geneList) <- (DE$GeneID) > head(geneList) FUN_000233 FUN_000410 FUN_000424 FUN_000451 FUN_000511 FUN_000590 TRUE...gene2GO) Error in .local(.Object, ...) : allGenes should be a factor or a numeric vector > I th…

R TopGO Geneenrichment

updated 5.3 years ago • AP

I know it is possible to do with the select command from the `` org.Mm.eg.db `` at least for one character vector. <pre> > head(select(org.Mm.eg.db, keys = my_list[[1]], columns = "ENTREZID", keytype = "SYMBOL")) SYMBOL ENTREZID 1 Abca1

org.mm.eg.db select list

updated 10.3 years ago • Assa Yeroslaviz

3358 3620 . + . ID=ex2;Parent=rna2;Name=E4exon2 HPV16_K02718_1_revised PaVE CDS 865 880 . + 0 ID=cds1;Parent=rna1;Name=E4cds1 HPV16_K02718_1_revised PaVE CDS...3358 3620 . + 2 ID=cds2;Parent=rna2;Name=E4cds2 HPV16_K02718_1_revised PaVE gene 2756 3853 . + . ID=E2geneid;Name=E2genename HPV16_K02718_1_revised PaVE mRNA...2756 3853 . + . ID=rna3;Parent=E2geneid;gene=E2;Name=E2rna1 HPV16_K02718_1_revi…

VariantAnnotation

updated 4.5 years ago • Kasper_holm2

div class="preformatted">Dear all, I have the following probe names selected from a dataset (GDS592), taken from GEO (SOFT format). gnf1m29878_a_at gnf1m13556_at gnf1m09610_a_at gnf1m11352_a_at...gnf1m26036_at ...more... And I want to get the GO term and Official Gene Name from these probe names. Is there a way to do it? I tried these two Bioconductor commands but fail. > library(…

GO probe GO probe

updated 17.4 years ago • Gundala Viswanath