Bioconductor Forum

I'm trying to use the NanoStringDiff package to perform a differential gene expression analysis However, when I try to construct the data set with the function NanoStringData = createNanoStringSetFromCsv(path, header = TRUE, designs), I keep receiving the error message "Error in rowSums(counts) : 'x' must be numeric" Here it follows a section from my datasheet: ``` Name Accession Neg…

Bioconductor Transcriptomics NanoStringDiff

updated 5.2 years ago • Pedro

xys.files) Loading required package: pd.hg18.60mer.expr Error in read.xysfiles(xys.files) : Must install the pd.hg18.60mer.expr package. In addition: Warning message: In library(package, lib.loc = lib.loc, character.only...xys.files) Loading required package: pd.hg18.60mer.expr Error in read.xysfiles(xys.files) : Must install the pd.hg18.60mer.expr package. Searching with Google, the only do…

updated 17.5 years ago • JEAN-YVES SGRO

rowData(example_sce) DataFrame with 2000 rows and 2 columns id gene_name <character> <character> Gene_0001 Gene_0001 ABC916 Gene_0002 Gene_0002 ABC794 Gene_0003 Gene_0003 ABC466 Gene_0004 Gene_0004...with my data is: ```r Error in intI(i, n = x@Dim[1], dn[[1]], give.dn = FALSE) : invalid character indexing ``` Bu…

scater

updated 4.2 years ago • enricoferrero

classes, fdef, mtable) :unable to find an inherited method for function ‘dbGetQuery’ for signature ‘"character", "character"’ Below are the exact commands: ``` > # specify the path to your sequence file: > fas <- "C:/Users/Hui Yi/Documents...fdef, mtable) : unable to find an inherited method for function ‘dbGetQuery’ for signature ‘"character", "character"’ ``` …

software error DECIPHER

updated 5.7 years ago • hoonhuiyi

Loading ideogram... Loading ranges... Error in .normarg_seqlengths(value, seqnames(x)) : the names on the supplied 'seqlengths' vector must be identical to the seqnames In addition: Warning messages: 1: In .local(x, ...) : 'track

biovizBase biovi

updated 2.3 years ago • bernatgel

I want to annotate gene names for a segmented file by finding overlap with it with a reference file. Would like to know how can it be done using

annotation

updated 10.5 years ago • seeker

I have expression data with Affymetrix hg u133 plus 2 probeset IDs & gene set data with gene names. So both gene set and expression data are not using the same gene ID system. Both gene set and expression data should use...is a requirement of the GAGE analysis. So the problem is that if i convert the Probeset IDs to gene name, i get a single gene name for multiple probes. So the expressio…

convert gage convert gage

updated 13.8 years ago • Javerjung Sandhu

<div class="preformatted">Hi all, I have a table (t) of the following format (first row is the header): A x1 x2 c 1 NA c 2 1002 c 3 NA a 4 1004 b 5 NA c 6 1006 c 7 1007 c 8 1008 b 9 1009 a 10 1010 a 11 1011 c …

updated 16.3 years ago • Hari Easwaran

read10xCounts(h5file). When I look at the rownames of the sce object (see below), the last 12 gene names are CMO301, CMO302 up to CMO312. These are the 10X genomics CMO tags that are used for tagging cells for cell multiplexing...The CMOs should not be added to the sce object as gene names. I could not find an option in read10xCounts to eliminate these rows (nor were google searches productive). …

DropletUtils droplet

updated 2.1 years ago • pcantalupo

columns=list(G="gMedianSignal", Gb="gBGMedianSignal", R="rMedianSignal", Rb="rBGMedianSignal"), names= targets[,"Names"], annotation = c("Row", "Col","FeatureNum", "ControlType","ProbeName", "GeneName")) I am trying to open Agilent 8x60K data...read.maimages is not able to read the file because all columns do not have some values (I mean some character in it). However, I am not an R expert, and …

Annotation limma Annotation limma

updated 14.8 years ago • Hari Easwaran

signature for generic sampleNames<- and classes LumiBatch, ANY cannot use with duplicate class names (the package may need to be re- installed) Error: loading failed Execution halted *** arch - x86_64 Warning: replacing previous...signature for generic sampleNames<- and classes LumiBatch, ANY cannot use with duplicate class names (the package may need to be re- installed) Error:…

Biobase lumi oligoClasses Biobase lumi oligoClasses

updated 13.4 years ago • Mark Cowley

Hello, I am using edgeR to calculate differential gene expression among individuals from two populations (BR and SD) exposed to three salinity treatments (15, 35, 60 ppt), with three biological replicates each (a, b, c) for 18 samples total. When I create my design matrix, my six treatments are named with numbers, but in the edgeR documentation, the treatments are named with letters, fo…

edger rnaseq glmlrt()

updated 10.8 years ago • MBWatson

contrast list. Depending on whether the design contains an interaction term, the effect/result names change, which makes it quite difficult to extract results in an automatic fashion (e.g. as part of a script or app, without

DESeq deseq2 resultsnames

updated 9.5 years ago • akaever

biological pathways between two classes of phenotypes. __I need help with printing out the pathway names for the resulting p-values that are found by miR2Pathway. But after looking at the igraph documentation I still cannot...do it. My code is error free, just hoping for some helpful suggestions.__ Additionally, the pathway names should join the miR2Pathway output, if run with the example datas…

igraph miR2Pathway Pathway page_rank

updated 7.7 years ago • genomic8328

create chromLocation object genome <- new("chromLocation") start <- data[,"start"] names(start) <- data[,"miRNA"] genome at chromLocs <- new("list",tapply(start,factor(data[,"chrom"]),I)) genome at organism <- "Homo Sapiens...create vector of mock data toPlot <- rep(1,length(data$miRNA)) names(toPlot) <- data$miRNA ## plot with cytobands represe…

Organism idiogram Organism idiogram

updated 17.2 years ago • Dykema, Karl

the function ReadAffy. The error is reproduced here: Error in validityMethod(object): No slot of name "phenoLabels" for this object of class "phenoData" I don't know what's wrong. Any help appreciated. thanks, suresh _________________________________________________________________

affy affy

updated 22.2 years ago • Suresh Kumar Karanam

Objective how to assign a col-name to an empty header inside a list My data structure Code should be placed in three backticks as shown below ```r results1...Objective how to assign a col-name to an empty header inside a list My data structure Code should be placed in three backticks as shown below ```r results1 &lt...lfcSE stat pvalue padj ``` M…

DESeq2

updated 3.7 years ago • kcm

seqnames ranges strand | gene_id <rle> <iranges> <rle> | <character> AT1G01010 Chr1 3631-5899 + | AT1G01010 AT1G01020 Chr1 6788-9130 - | AT1G01020 AT1G01030 Chr1 11649-13714 - | AT1G01030...Araport11_GFF3_genes_transposons.201606.gff Chr2 Araport11 gene 4674427 4674698 . + . …

GenomicFeatures genomicranges

updated 5.8 years ago • shangguandong1996

give an input csv file containing genes relevant.genes <- factor(as.integer(all.genes %in% data) names(relevant.genes) <- all.genes GOdata.BP <- new("topGOdata", ontology='BP', allGenes = relevant.genes, annotationFun = annFUN.db...affyLib = 'hgu133plus2.db') ------------ Error in .local(.Object, ...) : allGenes must be a factor with 2 levels > str(relevant.genes) F…

GO hgu95av2 GO hgu95av2

updated 12.8 years ago • Guest User

pairwise data I have. I've populated my hypergraph by creating hyperedges for each of my sample names that meet a pairwise threshold criteria with other sample names. For example: is sample_A shares a pairwise value of...hypergraph does not throw an error with the vCoverHypergraph() function. Therefore, there must be something awry with the kCoresHypergraph() function. If somebody could hel…

software error hypergraph

updated 6.1 years ago • john.horne

<div class="preformatted"> >Date: Fri, 12 Nov 2004 13:42:22 -0000 >From: "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> >Subject: [BioC] Confusion over limma documentation and design/contrast >To: "Gordon Smyth" <smyth@wehi.edu.au> >Cc: bioconductor@stat.math.ethz.ch > >Hi Gordon > >Thanks for the response. I…

GO Regression limma GO Regression limma

updated 21.1 years ago • Gordon Smyth

multiple times with each associated sample). See example code (only for MS Level 1) below: ```r # Vector with all sites # BM = Butte, Montana # GM = Glacier, Montana # PI = Pocatello, ID # SL = Salt Lake, UT # WU = Widtsoe, UT # FA = Flagstaff, AZ # TA = Tucson...containing .mzML files. Samples and their associated blanks should be in separate folders named "Sample" and "Blank". Depe…

xcms mzTab-M iterativehierarchicalprocessing FBMN

updated 2.6 years ago • Abrianna

<div class="preformatted">Hello Everyone, I am writing programs in R from 7 months and I am able to solve most of the errors/issues except for this current post. My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains the Microarray Expression Values collected from the Illumina Microarray experiment. These collected intensity values need to be normalized(Rank Invariant…

Microarray Normalization Microarray Normalization

updated 17.8 years ago • Suprabhath Reddy Gajjala

I'm trying to work with TCGAbiolinks, but I get an error with TCGAanalyze\_Normalization. I would appreciate any help troubleshooting this. Commands: >SKCM\_query<-GDCquery("TCGA-SKCM",data.category="Transcriptome Profiling",data.type="Gene Expression Quantification",experimental.strategy="RNA-seq",access="open",sample.type=c("Primary solid Tumor","Metastatic"),workflow.type="HTSe…

tcgabiolinks error

updated 9.0 years ago • salvl

GenomicRanges

updated 20 months ago • mat149

If I use the same format with multiple IDs, it returns an error: ```r Error in vapply(names(filterChunk), FUN = function(filter, values, mart) { : values must be length 1, but FUN(X[[2]]) result is length 2 ``` But if I only gives a

Annotation biomaRt

updated 2.6 years ago • RuBBiT0

the work mac. Here is my session (I has to eliminate part of the sessionInfo() to stay within character limit. Please raise the character limit): ``` > results.ranges <- extractRanges(DMRs, genome = "hg19") snapshotDate(): 2020...0%Error: failed to load resource name: EH3132 title: hg19.generanges reason: 1 resources failed to download In addition: Warning mess…

DMRacte DMRcateranges ExperimentHub hg19.generanges

updated 5.0 years ago • richardallenfriedmanbrooklyn

call: .make_BSgenome_seqinfo(single_sequences, circ_seqs, genome, seqnames) error: sequence names found in file '/Users/Geo/BSgenome.Dmelanogaster.6.32.Rcheck/00LOCK-BSgenome.Dmelanogaster.6.32/00new/BSgenome.Dmelanogaster.6.32...Check seqnames. current_SequenceName <- unlist(heads(strsplit(names(dna), " ", fixed=TRUE), n=1L)) names(dna) <- current_SequenceName ### Export …

BSGenome Forge

updated 4.1 years ago • geo.vogler

analysis to identify potential biomarkers. Here is a section of my datasheet: ``` CodeClass Name Accession Epi_FAM1.1 Epi_FAM1.2 Epi_FAM2 Epi_FAM3 Positive POS_A(128) ERCC_00117.1 77244 77495 66892 68724 Positive...1230 ``` When I try to creat the set I get the error Error in rowSums(counts) : 'x' must be numeric, so I cannot proceed…

NanoStringDiff

updated 6.6 years ago • noelleenright

values: phenoData(normData) <- pheno The rownames of phenodata has the samples names: rownames(phenoData(normData)) [1] "GSM437316" "GSM437286" "GSM437305" "GSM437297" "GSM437277" "GSM437282" "GSM437269" "GSM437302...GSM437311" [12] "GSM437218" "GSM437114" "GSM437234" "GSM437165" "GSM437299" But column names of assaydata are file names: colnames(exprs(no…

oligo GEOquery ExpressionSet

updated 6.2 years ago • salamandra

b.score c.score cohort subtype 57 <numeric> <numeric> <numeric> <character> <character> 58 [1] 0.263871 0.408836 0.269231 NYC B 59 [2] 0.239878 0.400169 0.250000 NYC B 60 [3] 0.262476 0.436118 0.250000...b.score.x c.score.x cohort.x subtype.x 89 <numer…

GenomicRanges plyranges

updated 3.5 years ago • Rodrigo

Hello, I have an inquiry on how to apply the "paCalls" function of the oligo package.  I received a wicked error message after running the "paCalls(CELdat, "PSDABG")" line which states:  Computing DABG calls... Error in 0:max(counts) : result would be too long a vector In addition: Warning message: In max(counts) : no non-missing arguments to max; returning -Inf I am un…

oligo

updated 7.9 years ago • mat149

R * inst ** byte-compile and prepare package for lazy loading Error in RccViolationException("Class names must begin with a letter: ", : > "RccViolationException" function can not be found Error: unable to > load R code in package...gt; byte-compile and prepare package for lazy loading Error in > RccViolationException("Class names must begin with a letter: ", : >…

TCGAbiolinks R.oo

updated 5.4 years ago • Talip Zengin

fine for me. However, when I use it now, I get the error, "invalid class “DESeqDataSet” object: 'NAMES' slot must be set to NULL at all time". This can reproduced using the example dataset given on pages 5-6 of the "Analyzing RNA...design = ~ condition) Error in validObject(.Object) : invalid class “DESeqDataSet” object: 'NAMES' slot must be set to NULL at all time</pre>   I …

deseq2 error

updated 10.5 years ago • alextuck

a bug. The paste generic defined in BiocGenerics seems to behave weirdly when 'lapply'd to a list of character vectors. A simple example follows: Starting from a fresh R session: <pre> library(BiocGenerics) aa = list(letters[1:10...1] "k" "l" "m" "n" "o" "p" "q" "r" "s" "t"</pre>   The expected result is to collapse both vectors into a single string, as base::paste does…

biocgenerics

updated 8.4 years ago • Peter Langfelder

TRUE) In fact, after this step I have noticed that ProbeNames are not matching the right miR names. This happens starting from both the dataset supplied as an example and my own miRNA microarray data. The match is correct

miRNA Microarray Normalization AgiMicroRna miRNA Microarray Normalization AgiMicroRna

updated 14.9 years ago • Paola Ostano

species='Mus_musculus') >>> Reading CDF file. >>> Error: cannot allocate vector of size 1 Kb >>> Execution halted >>> >>> _______________________________________________ >>&gt

Cancer cdf Cancer cdf

updated 16.0 years ago • Martin Morgan

des2Report) and I have this error: Error in results(object, resultName) : 'contrast', as a character vector of length 3, should have the form: contrast = c('factorName','numeratorLevel','denominatorLevel'), see the manual

Deseq2 reportingtools

updated 11.1 years ago • jarod_v6@libero.it

ENSG00000000005' ############################# d <- read.table("count.txt", colClasses = c(rep("character",1),rep("integer",2), rep("null",126)),header=TRUE) Error in methods::as(data[[i]], colClasses[i]) : no method or default for coercing...character" to "null" > d <- read.table("count.txt", colClasses = c(rep("character",1),rep("integer",2), rep("NA",126)),header=TRUE) …

updated 13.7 years ago • Guest User

Dear Dr Peter and WGCNA collegues, Thanks collegues in genetics.ucla.edu for sharing WGCNA package for co-exp analysis. But we are confused about the page margin setting, sth like shuffling the rows and columns, mentioned in Figure2 of "<span style="background-color:Yellow">https://support.bioconductor.org/p/67548/</span>" (https://support.biocond…

WGCNA plotNetworkHeatmap par

updated 9.2 years ago • boyashuang

raw.exac.AN.adj.)) # make the allele counts into a plain data frame - chr positions are only row names and not their own column df.exac.AC.adj <- as.data.frame(sclass.exac.AC.adj) df.exac.AN.adj <- as.data.frame...sclass.exac.AN.adj) # make the chr positions an actual column and remove the row names to make it cleaner df.exac.AC.adj$chr.position <- row.names(df.exac.…

R variantannotation vcf scanvcfparam readvcf

updated 9.6 years ago • emily.mccann

start") = 0; ranges.slot("width") = 2; char strand = '+'; //Strand string names = "abc"; //Names of GRanges G.slot("seqnames")= seqnames; G.slot("ranges")= ranges; G.slot("strand")= strand; return G; }</pre> Error is this...invalid class “GRanges” object: 2: invalid object for slot "strand" in class "GRanges": got class "character", should be or extend cl…

GRanges IRanges RCPP Constructor

updated 8.2 years ago • hauken_heyken

Warning messages: 1: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 2: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 3: In curl::curl_fetch_disk...url, x$path, handle = handle) : progress callback must return boolean 4: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress …

annotationhub

updated 10.2 years ago • acaugu

Revision: 86351 Author: m.lawrence Date: a day ago Paths: Modified /trunk/madman/Rpacks/IRanges/R/Vector-class.R<https: bioconductor="" hedgehog.fhcrc.="" iranges="" madman="" org="" r="" rpacks="" trunk="" vector-class.r=""> Modified /trunk/madman...hedgehog.fhcrc.org="" ioconductor="" iranges="" madman="" rpacks="" trunk=""> generalize eval() to Vectors, add as.env,Vector that fo…

Cancer IRanges GenomicRanges PROMISE Cancer IRanges GenomicRanges PROMISE

updated 11.9 years ago • Malcolm Cook

when I get the error: Error in order(MA$genes$Chr, MA$genes$Position) : argument 2 is not a vector The processCGH function is expecting to see a column named Position. (You can see this if you look at the line ord <- order...function) However, processing the Agilent input files with readPositionalInfo(), I get columns named Chr, Start, End. Am I ok if I simply rename the Start column…

CGH snapCGH CGH snapCGH

updated 16.3 years ago • Dick Beyer

vs > knockdown comparison > > Targets file: > SlideNumber ArrayNumber FileName Name Cy3 Cy5 > 1 1 Input/1_1.txt 1_1 Scramble Knockdown > 1 2 Input/1_2.txt 1_2 Knockdown PC3M > 1 3 Input/1_3.txt 1_3 PNT2...PNT2 > > PC3M = the control cell line > Kno…

Microarray Cancer limma Microarray Cancer limma

updated 17.1 years ago • Yannick Wurm

c(keep0 = 4095L, keep1 = 4095L), simpleCigar = FALSE, reverseComplement = FALSE, tag = character(0), tagFilter = list(), what = character(0), which = new("CompressedIRangesList", unlistData = new("IRanges", start = integer(0), width...integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()…

dba.count DiffBind ATACSeq

updated 2.2 years ago • sophie.hfliu

these events have taken place within the boundaries of genes, and I would like to retrieve the gene names (ensemble ID). I've tried to use biomaRt: > getBM(attributes=c("ensembl_gene_id"),filter=c("chromosome_name","star t","end"), values

updated 16.0 years ago • Boel Brynedal

<div class="preformatted">Dear Sir/Madam,      Here I have two question.      First is  when I run  R in the computer, I found the computer appeared wrong message "Error: cannot allocate vector of size 214.5 Mb", what is its mean? Would you kind to  give me more suggestion?  &nbsp…

updated 16.2 years ago • Sun Wei

have a table with expression values for 2000 genes, for 16 samples, rownames are EntrezGeneIDs and a vector which contains the signature, +1 or -1 for 200 genes, names are EntrezGeneIDs. So I wanted to get the activity scores, but

DART DART

updated 11.8 years ago • Guest User

Hello everyone, I have problems getting the flowClust.2d to work. <pre> library(flowViz) library(openCyto) data(GvHD) fr <- GvHD[[2]] trs <- logTransform() fr_trans <- transform(fr, `FL1-H` = trs(`FL1-H`), `FL2-H` = trs(`FL2-H`)) fr_trans fres <- flowClust.2d(fr = fr_trans, xChannel = "FL1-H", yChannel = "FL2-H", K = 2, target = c(3,2)) </pre>…

opencyto flow cytometry

updated 9.7 years ago • Ulrik Stervbo

with the last update) that the read.flowSet function no longer maintains the order of the file vector given to it but instead automatically sorts on file name. This behaviour is increadibly annoying and makes the function

flowcore flowcytometry

updated 10.4 years ago • Jiang, Mike

gt; ## what type of info is available? > > > dbGetQuery(con, "select * from snp129 where name='rs25';") > bin chrom chromStart chromEnd name score strand refNCBI refUCSC observed > 1 673 chr7 11550666 11550667 rs25...select name, chrom, chromEnd, observed, func from snp129 > where name in ('", paste(rsid, collapse = "','"), "');", sep = "") > …

SNP affy biomaRt rtracklayer SNP affy biomaRt rtracklayer

updated 15.7 years ago • James W. MacDonald

rows and 5 columns study id source final_description group_nr <character> <character> <character> <character> <factor> GSM4447088 GSE147851 GSM4447088 ATRT patient tumor BT12,SMARCB1 1 GSM4447089...s/legp4s7ek0704uw/dds.RDS?dl=0 [3]: /media/images/0121be9b-6830-4f38-b1e3-c3249c00</factor></c…

sva

updated 3.5 years ago • shdam

space ranges | peak strand feature start_position end_position <character> <iranges> | <character> <character> <character> <numeric> <numeric> 01 YAL069W I [ 16, 254] | 01 1 YAL069W 335 649 02 YAL067W-A I [ 2731...survival_2.35-8 tools_2.11.0 XML_2.8-1 …

Yeast ChIPpeakAnno Starr Yeast ChIPpeakAnno Starr

updated 15.6 years ago • Noah Dowell

gene_description Expr <rle> <iranges> <rle> | <character> <character> <character> <character> <numeric> OR4F5 chr1 69091 + | ENSG00000186092 protein_coding OR4F5 olfactory_receptor...just the closest. Any help would be much appreciated! </integer></integer></integer>&…

R GenomicRanges Granges

updated 5.9 years ago • ssabri

readCtData(files="combined_file.txt", n.features=768, n.data=24, ...) Obviously, the your file names can be called whatever you want them to; these are just examples for simplicity. > - Each .txt must have miRNA name and Ct...or failed the quality control) etc. > - Moreover .txt for each sample I need a .txt with samples names and group?? > You'll need some sort of mapping…

miRNA qPCR PROcess HTqPCR miRNA qPCR PROcess HTqPCR

updated 13.5 years ago • Heidi Dvinge

gt;> id exon transcript gene symbol density >> <rle> <iranges> <rle> | <character> <character> <character> >> <character> <character> <character> <numeric> >> [1] chrVIII [212510, 212704] + | CDS unknown &gt...Integrative Genomics Princeton Uni…

Annotation Gviz Annotation Gviz

updated 11.6 years ago • Lance Parsons

If I would like to represent a protein sub-network, what is the best data structure for it? It has the flat file format:   <table align="center" border="1" cellpadding="1" cellspacing="1" style="width:25%"> <tbody> <tr> <td><strong>Hub</strong></td> <td><strong>Interactor</strong></td> </tr> <tr> <td&…

AnnotationDbi Bimap Interactome

updated 7.7 years ago • Dario Strbenac

matrix. If provided, design matrix should also ## ## be provided.It's a vector of 0, -1, 1, with names matching ## ## column names of the design matrix. ## ## - designMatrix: the design matrix used for running the glm...filter: return new filtered dge list for fitting to ## ## the model and the "keep" vect…

genefilter edgeR

updated 9.7 years ago • cafelumiere12