Bioconductor Forum

OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Warning messages: 1: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular 2: Named parameters not used in query: internal_id...name, type, chrom, strand, start, end 3: Named parameters not used in query: internal_id, name, chrom, strand, start, end 4: Named parameters...not used in query: i…

genomicfeatures

updated 8.8 years ago • layal8785

the related normalization functions: normalize.constant, normalize.loess, normalize.quantiles (to name a few). Normalize.invariantset, unlike the other functions mentioned, does not accept as its input a matrix of expression...values, but rather a vector of expression values (presumably from one chip), as well as a vector of expression values against which to normalize...a list of length 2 comp…

updated 22.0 years ago • david neil hayes

results in excel, the column header was missing on the final column. The column header for probset name was actually the name of the first array. When I normalized using RMAexpress, I could see that the problem was that the probset...name was missing and all the names of the arrays were shifted to the left. Should I simply insert the probeset column header

updated 22.5 years ago • Haddad, Ramsi

I can provide these information by pasting a list of identifiers, so the requested information must be somewhere in the tables. My found solution is kind of indirect by first getting a table of all UCSC names together with...gene symbols, finding the corresponding UCSC names to my symbols and then searching these UCSC names in a table of all UCSC names with location. Thank you in advance, Chris…

rtracklayer rtracklayer

updated 16.5 years ago • Christian Ruckert

a simple button that I would like to be associated with the "fileBrowser" function (returning a vector of file names). >library(tkWidgets) >browserButton<-button(wName="browserButton",wValue="Browse",wEnv=glob alenv...fileBrowser seems to work fine, I select some files, but I'm not able to retrieve the "returned" vector of file names.. > test at pWidgets[[1]][[1]]@wV…

DynDoc tkWidgets reposTools widgetTools DynDoc tkWidgets reposTools widgetTools

updated 19.9 years ago • mattia

<div class="preformatted"> Dear All, Appreciate your time. Need your expertise. I am trying to use GOSeq for GO analysis of my RNA-seq experiments. I was using Tophat->Cufflinks for DE, and mouse mm10 for annotation. I am trying to build the gene length database by myself, given that the current version of goseq does not support the mm10 build. 1, Cufflinks seems ignored the orig…

Annotation GO PROcess goseq Annotation GO PROcess goseq

updated 12.6 years ago • Guest User

preformatted">Hi, I get "Error in sqliteExecStatement(con, statement, bind.data) : , bind.data must have non-zero dimensions" when run. It seems similar this error https://stat.ethz.ch/pipermail/bioconductor/2011-February...ndf", full.names = TRUE) #################################################### ## Make info package MUST have only one POS and ## ## NDF file in the directory …

BiocViews Annotation Organism biocViews BiocViews BiocViews Annotation Organism biocViews

updated 13.9 years ago • mabawsa

Hi Paul, MArrayLM objects subset in the same way as other objects in R (data.frames, matrices, named vectors etc), and that was a deliberate design decision. All of them can be subsetted using logical, character or numerical

limma limma

updated 17.5 years ago • Gordon Smyth

gene_association.tair") : At least one DB object ID has multiple DB object symbols or names in gene ontology annotation file. In addition: Warning messages: 1: In result_fetch(res@ptr, n = n) : SQL statements must be issued...of dbGetQuery() or dbSendQuery(). 2: In result_fetch(res@ptr, n = n) : SQL statements must be issued with dbExecute() or dbSendStatement…

goseq rnaseq r

updated 5.2 years ago • citronxu

div class="preformatted">Hello, The latest version of arrayQualityMetrics names the arrays "1, 2, 3...". How do I know which number corresponds to which .cel file? In previous versions the name was the .cel file...name. Why the change? --- Dr. Ricardo A. Ch?vez Montes Laboratorio Nacional de Genomica para la Biodiversidad CINVESTAV-IPN Km. 9.6

arrayQualityMetrics arrayQualityMetrics

updated 14.3 years ago • rchavez

of bounds Could you please help me to fix this? Thanks, emily -- output of sessionInfo(): > names(bedlist)=NULL > allorigins=do.call(c, bedlist) > allorigins=sort(allorigins) Error in x[!nas] : selecting spaces: subscript...with 258508 rows and 1 value column across 240 spaces space ranges | name <factor> <iranges> …

GenomicRanges GenomicRanges

updated 12.7 years ago • Guest User

I import data from JSON file which contain squence names and DNA sequences, and other things. How do I make multisequence alignment, extracts positions that has SNPs (flanking...each end of a SNP with some character, 'N' or '-' for easy differentiation), and visual the alignment in a graph (i.e. ggplot

msa Biostrings

updated 5.7 years ago • Vang Le

dear all! So basically what I have are two numerical vectors: <pre> A <- c( 1, 2, 3, 4, 6, 7 ) B <- c( 8, 9, 10, 11, 12, 13 )</pre> and I would like to combine them so that the result would be: 1, 8, 2, 9, 3, 10, 4, 11, 6, 12, 7, 13

basic R

updated 11.0 years ago • Johannes Rainer

<div class="preformatted">Hi all, I need to extract information from the library ath1121501. I would like to obtain a list to have a correspondance between GO terms and the gene names. The list should be such that the names of the list are the gene names (AT4G19650" ,"AT5G47010", etc...) and each member of the list contains the vector of all the terms GO in which the gene is affected. The…

GO ath1121501 GO ath1121501

updated 19.2 years ago • Martin Olivier

be able to assign this variable as name to the `HeatmapAnnotation` object (that defines the column annotations). I cannot do the following since the name of the...col = list(Species = col_vector)) Instead, what I try to do is to use a placeholder name, and then try to change `column_ha` name with `my_var`, like this: col_list <- list(VAR = col_vector) names(col_list) &…

ComplexHeatmap

updated 21 months ago • daniel.carbajo

Hello, I was doing normalization step in R but it is showing me this error.. ``` >names=dir(pattern="CEL.gz") > My_CELdata=ReadAffy(widget=TRUE) Error: cannot allocate vector of size 2.6 Gb > My_CELdata=ReadAffy...selectView))[1] != "") { : missing value where TRUE/FALSE needed Error: cannot allocate vector of size 2.5 Gb ``` So how to proceed further now

normalization

updated 5.8 years ago • manuchandwadkar

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updated 18.7 years ago • Lana Schaffer

geneFile <- "genefile.txt" uniFile <- "universe.txt" universe <- scan(uniFile, what="character") genelist <- scan(geneFile, what="character") pcut <- 0.05 catSize <- 5 params <- new("GOHyperGParams", geneIds=genelist...Ben -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: universe.…

GOstats GOstats

updated 16.4 years ago • Benoit Ballester

metadata info please help me is it a bug or I am doing anything wrong even though i have same number names as columns still getting a error Thank you ``` tpm_count <- read.table("TPM.tsv", sep="\t", header=T, row.names=1) dim(tpm_count...tpm_count), colData=DataFrame(label=cell.labels) ) ) **Error in method(object) : all assays must have the same nrow and ncol** sessionInfo( ) R ve…

SingleCellExperiment scran scater

updated 3.7 years ago • Lucky

error message: "Error in asMethod(object) : all the ranges in the object to coerce to GPos must have a width of 1" Can someone help us understanding where is our error, and how to correct it ? Here is the code: library(CAGEfightR...ix] rownames <- str_extract(sampnames, "W|H") design <- data.frame(row.names = sampnames, Name = sampnames, BigWigPlus = bw_plus, BigWigMin…

CAGEFightR CAGE CTSS

updated 6.7 years ago • July

I have time-course data as "Day1", "Day2"....., when I create the list for compareCluster(), I have named the order as levels(list) = c("Day1","Day2"....), and I check the compareCluster() result, CompGO@compareClusterResult$Cluster, shows...the order is "Day1", "Day2".... However, when I plot the data, the X-axis show the disorder characters. How can I fix the problem

clusterProfiler

updated 8.7 years ago • joseph

27998): ENSMUSG00000051951 ENSMUSG00000089699 ... ENSMUSG00000096730 ENSMUSG00000095742 rowData names(2): id symbol colnames: NULL colData names(2): dataset barcode reducedDimNames(0): spikeNames(0):</pre> and I would like to use...log2( + calculateCPM(sce10x, use.size.factors = FALSE) + 1) Error in colSums(counts_mat) : 'x' must be an array of at least two dimensions</pre&g…

scater SingleCellExperiment

updated 8.3 years ago • chriad

and I get an error of  <pre> Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'</pre> I looked through the code displayed when calling DEXSeqResults to no avail, and am feeling a bit stuck...sample + exon + Treatment:exon Ldxd = DEXSeqDataSetFromHTSeq( countfiles = Leaf, # vector of count file names sampleData = DescLeaf, …

dexseq

updated 10.5 years ago • Sam McInturf

Hi, I want to perform a biomaRt query on my RNASeq dataset to match the ensembl version ID to the hgnc symbol (for approx 1300 genes). ``` library("biomaRt") listMarts() listEnsembl(verbose=TRUE) ensembl = useEnsembl(biomart="ensembl", dataset = "hsapiens_gene_ensembl", mirror="uswest") mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl", dataset = "hsapiens_gene_ense…

biomart

updated 5.7 years ago • bak16

<div class="preformatted"> Has anyone used the mogene10stprobeset.db annotation package? I have a list of significant probeset ids that I obtained from running an analysis in the limma package. When I try to use mget() to retrieve the corresponding gene names only a couple of probesets get annotated. I've tried with several different gene lists. In a gene list of about 300 genes, only 2 ge…

Annotation GO hgu95av2 probe limma Annotation GO hgu95av2 probe limma

updated 13.2 years ago • Guest User

I want to add a column with name "category" to my data, how can i do that? input: col1 col2 col3 col4 col5 1 20 + 4 6 2 24 - 6 7 .... output: col1 col2 col3 col4 col5 col6 1 20

name R column

updated 2.8 years ago • sat

and i am ending up with following error. Cy3.norm <- apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x ,na.rm=TRUE)})}) Error in tapply(v, names(v), function(x) { : arguments must have same length any help is appreciated

miRNA miRNA

updated 15.4 years ago • ashwin Vishnuvardhana

Since the latest FlowCore update, when I try to rename the $PnS parameters those marker names are not saved to my file when writing FCS files. However, when I rename $PnN parameters the marker names do get saved to file

flowCore

updated 4.8 years ago • jasonemo

In the bioconductor tutorial for gviz I have noticed that sometimes the name of a track disappears from the plot if the track is small. Is it possible to set the minum height of the track, so that the...name of the track does not disappear (is independent of the track height) ... or is it possible to set the minimum size of the legend

gviz

updated 10.7 years ago • tonja.r

rqcResultSet)\`   I get the following error: Warning: Error in eval.quoted: envir must be either NULL, a list, or an environment. Stack trace (innermost first):     107: eval.quoted     106

software error bug library

updated 8.9 years ago • guus.steeg

which would normally be some test to do with a p-value or other score) and to specify allGenes as a named factor, where the probeset is 1 if I consider it interesting, and 0 otherwise. In the code snippet below, `exprset` is an ExpressionSet...is "interesting" and 0 otherwise geneList <- factor(as.integer (all_genes %in% interesting_genes)) # name the factor with the probeset names names (…

Microarray GO topGO Microarray GO topGO

updated 15.4 years ago • Mike Dewar

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updated 19.8 years ago • Gaj Stan BIGCAT

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updated 18.3 years ago • Brooks, Anthony B

with supportedOrganisms() from goseq: __Error in matrix(unlist(pairs), nrow = 2) :   'data' must be of a vector type, was 'NULL'__ Is there something I am doing wrong? Many thanks in advance!! Victoria R version 3.3.2 (2016...Loading required package: GenomeInfoDb Error in matrix(unlist(pairs), nrow = 2) :   'data' must be of a vector type, was 'NULL' &g…

go goseq

updated 8.8 years ago • starbug16

stage", c("S2","S3","S4"), "S1")) Error in checkContrast(contrast, resNames) : 'contrast', as a character vector of length 3, should have the form: contrast = c('factorName','numeratorLevel','denominatorLevel'), see the manual

deseq2

updated 8.2 years ago • thibault.lorin34

always shown error msg as "Error in as.vector(x, mode) :   cannot coerce type 'closure' to vector of type 'any' ". The input gene ID is gene symbol, and character format, it looks like as below: > str(list\_GeneSymbol) &nbsp

clusterProfiler

updated 9.3 years ago • joseph

function can take either a blocking factor or a design matrix. Would the blocking factor simply be a character vector of cell cycle assignments (e.g. G1, G2M, or S) and the design be the same matrix of covariates as supplied to the

scran

updated 6.3 years ago • s1437643

<div class="preformatted"> Hmm..I forgot. In our function we use the vennDiagram function which is a part of the limma package. So U must have that package loaded. /M Hi. At our department we have made a small vennDiagram script. I am not sure if it suites your needs...I forgot. In our function we use the vennDiagram function which is a part of the limma package. So U must have that pack…

updated 21.7 years ago • Marcus

reasons that I'm not sure I understand, the argument list used in the definition of this S4 method must start with 'x'. The consequence of all this is that dispatch will happen on 'x' so if named arguments are passed with a name that...length 0 > c(a=IRanges(), x=IRanges()) IRanges of length 0 But when all the arguments are named with names != 'x', then nothing is passed to 'x' and…

Cancer IRanges BiocGenerics Cancer IRanges BiocGenerics

updated 13.1 years ago • Hervé Pagès

DataFrame with 2 rows and 2 columns > id seqs > <character> <dnastringset> > 1 ID1 AAATG > 2 ID2 GT > > as.data.frame(df) > > Error in as.data.frame.default(y, optional...Micha…

Cancer Biostrings GLAD Cancer Biostrings GLAD

updated 14.2 years ago • Hervé Pagès

Hi, As the name implies, longestConsecutive() finds the longest match of a character efficiently in Biostrings. I dont know any other

Biostrings

updated 19 months ago • Ali Osman

the DNA sequences in 'x' by those in 'y'. i can imagine how to do it coercing back and forth to character and so on but i guess there must be some more efficient way to do it. my interest come from the fact that the DNAStringSet

updated 12.3 years ago • Robert Castelo

div class="preformatted">Hi, suppose I have a list of gene names like below, is there a "fuzzy"-matching based algorithm to convert gene name to locuslink id's? > head(anno[,4]) [1] Comp Rheb Ctsj

convert convert

updated 18.6 years ago • Weiwei Shi

allocator<unsigned="" std::vector<unsigned=""> > > > >' has no member named 'begin' incrConnComp.cpp:71: error: 'struct std::pair<boost::detail::component _index_iterator...allocator<unsigned="" std::vector<unsigned=""> > > > >' has no member named 'end' incrConnComp.cpp:76: error: 'struct std::pair<boost::detail::com…

updated 15.2 years ago • Bernt Guldbrandtsen

this: samples <- RangedDataList(RR05ranges,RR06ranges,RR2_03ranges,RR2_04ranges) Can i assign names like this? names(samples) <- c("RR05","RR06","RR2_03", "RR2_04") It works, but my worry is that the order might be different if objects...do not have a fixed order..... Or is there a way of assigning a name to each RangedData object before they are added to a list? Thank you! As …

htSeqTools ASSIGN htSeqTools ASSIGN

updated 14.0 years ago • Ian Donaldson

tbody> <tr> <td> <p> </p> </td> <td> <p>I´m using bioconductor and I want to extract the tissue name of the cel files (not the file name itself because a lot of cel files with different names can be related to the same tissue...in order to create a principal component analysis scatter plot where each group name is equals to tissues names. I do…

pca oligo cel

updated 10.5 years ago • angel.ruvalkba

CEL files using: >data.test<-ReadAffy(widget=TRUE) So I would like to look at the first sample name of my data: >sampleNames(data.test[1]) [1] "C:/Program Files/R/rw1090/rdata/JS1999081101AA.CEL" Why are the sample names displayed

updated 21.7 years ago • Vitalina Komashko

to tell where you are having problems. My guess is that you are not appending an additional 'GS' row name to your new vector of row names. If we take the example from page 2 of the vignette, the plot call is smcPlot(pg[,],sub,scale=c(-12...Notice the row names are reversed (E -> A insead of A -> E). This happens in smcPlot code. If you type smcPlot you will see the source code an…

GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA

updated 14.4 years ago • Valerie Obenchain

ug") Error in read.table(file = file, header = header, sep = sep, quote = quote, : 'file' must be a character string or connection How to import my table (GGal_ID_UG.txt) as a character string or connection? Is there

Annotation affy Annotation affy

updated 14.8 years ago • Dana.Stanley@csiro.au

in transformRNAseq(y = y, normFactors = normFactors, transformation = "profile", : ‘normFactors’ must be one of the following: none, TC, DESeq, TMM, or a vector oflength equal to the number of columns in ‘y’ ``` Looking at the code, I did

coseq rna-seq

updated 6.8 years ago • varunorama

1]]$sys, Ontology="BP", removeRoot=TRUE,chip="org.Sc.sgd.db") where "hits.list[[1]]$sys" is a vector containing yeast genes. -- output of sessionInfo(): Here is the error message: "Erreur dans .get_eg_to_go_fun(mapfun, chip...either mapfun or chip must be specified De plus : Message d'avis : objet 'org.Sc.sgdGO2PROBE' introuvable DB-based version of org.Sc.sgd.db not found

Yeast graph GOstats Yeast graph GOstats

updated 11.8 years ago • Guest User

lt;- readDNAStringSet("~/piRbase.fa") fasta@ranges group start end width names 1 1 28720989 28721013 25 piR-hsa-1000547 2 1 42817439 42817467 29 piR-hsa-1483697 3 1 43210296 43210328 33 piR-hsa-1497078...30 piR-hsa-1732223 fasta A DNAStringSet instance of length 29 width seq …

biostrings fasta genomicranges granges

updated 6.9 years ago • Konstantinos Yeles

Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData > Could you please help with it, Galina

BatchQC batchinDeseq2. columnsincolData.

updated 19 months ago • Galina

I went through to your doc* and I searched a lot on ncbi, internet to find out what is the full name of these columns? You must have it somewhere, all serious scientific work always give the full names of the abbreviations...I went through to your doc* and I searched a lot on ncbi, internet to find out what is the full name of these columns? You must have it somewhere, all serious scientific wo…

ChAMP

updated 5.8 years ago • julie

0 2 319 30 524 3 0 0 0 ``` As you can see, the gene names have been removed, replaced by single-digit numbers. My supervisor says these are placeholders. My issue is that when...I create the dds objects, there are no gene names present - it is just the "placeholders". This naturally causes issues when I try to annotate my DESeq results using biomaRt.…

DESeq2

updated 16 months ago • Olivia

the tximport pipleine for RSEM like following but when I checked the rownames, it gave me gene names instead of transcript names  <pre> rsem.files=list.files(".","*.isoforms.result") txi.rsem=tximport(rsem.files, type

tximport rsem

updated 8.3 years ago • deena

Ref ID and I want to get the rs# for these SNPs, is there an R package that can help me find the SNP name for each corresponding SNPRefID. I am  using SNPlocs.Hsapiens.dbSNP.20080617 package to find the SNP locations

SNP Homo sapiens SNPlocs SNP Homo sapiens SNPlocs

updated 16.6 years ago • Kay Jaja

reads the data sample sheet which has basic Sample\_name, Slide etc, I get error in Basename column name ( which is not there in my sample sheet).  The sample sheets of my other datasets did not have any specific "Basename" column...nbsp;                         __ charac…

methylation minfi

updated 9.2 years ago • parap

subset=TRUE, span=0.4, Mloc=TRUE, Mscale=TRUE, echo=FALSE, ...) subset: A logical or numeric vector indicating the subset of points used to compute the normalization values. But HOW? ;-) What form of vector? is it: i) the name...indicating whether to use that row of data in the normalisation (1) or not (0)? ii) an independent vector full of 1's and 0's, in the SAME order as the data in the m…

Normalization Normalization

updated 22.4 years ago • michael watson IAH-C

cond<-c(cond,u)   pairs\_edge\[\[counter\]\]<-cond   counter<-counter+1 } names\_edge<-names(table(design$Condition)) if(length(names\_edge)==2){   if(names\_edge\[1\]==pairs\_edge\[\[1\]\]\[1\]){     intercept...lt;-names\_edge\[2\]   }else{     intercept…

deseq2 edger differential gene expression additive model

updated 10.0 years ago • jlerga