Bioconductor Forum

div class="preformatted">Dear BioCers, Anyone that could shed light on the error- "Parameter names must by syntactically valid names in R" -would be greatly appreciated. Google turned up were these relevant findings...https://stat.ethz.ch/pipermail/bioconductor/2008-March/021440.html -which suggested spaces in names could yield such errors. I failed to find such spaces in my targets fil…

updated 15.2 years ago • k. brand

X4_Frozen,X11_RNAlater,X12_RNAlater,X13_RNAlater,X14_RNAlater)) #X1_Frozen etc. = equals row names/groups design = model.matrix(~0+cond) design = model.matrix(~0+cond) colnames(design) = gsub("cond","",colnames(design)) contrast...makeContrasts(contrasts=x,levels=design) When trying to run the contrast command I'll get the following error message: Error in makeContra…

limma

updated 4.7 years ago • mjensen2

gt; cont.matrix= makeContrasts(MT_3hvsMT_0h= (M_A3h+M_D3h+M_G3h+M_K3h- (M_A0h+M_D0h+M_G0h+M_K0h))/4, levels=design) Error in makeContrasts(MT_3hvsMT_0h = (M_A3h + M_D3h + M_G3h + M_K3h - : Parameter names must by syntactically valid...names in R But my same command had worked on a reduced dataset just a few days earlier. Turns out the issue came from my targets...gt; cont.matr…

limma limma

updated 17.1 years ago • Yannick Wurm

Here is what I am doing, after creating the design matrix, I am trying to create the contrast matrix ```r # > sample <- factor(rep(c("Non neoplastic","Tumor"), each=21)) > design.mat <- model.matrix(~0+sample) > colnames(design.mat) <- levels(sample) > design.mat Non neoplastic Tumor 1 1 0 2 1 …

RNASeqR

updated 4.1 years ago • Rishav

a contrast to see which are DE. I have tried to do this as follows: design<-factor(levels(probe.type1)) design<-model.matrix(~0+design) dim(design) dim(E.ncRNA1) subE.ncRNA1<-E.ncRNA1[ ,1:12] fit<-lmFit(subE.ncRNA1...design) contrast.matrix <- makeContrasts(<code>piRNA-miRNA, </code>levels=design) …

limma design and contrast matrix

updated 9.0 years ago • christopher.clarskon15

When I used beadarry and limma packages to perform differential gene expression analysis on the GSE49454 data set, I stuck to this group name and tried a lot of methods. url<-"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49454/matrix/" filenm<-"GSE49454\_series\_matrix.txt.gz" if(!file.exists("GSE49454\_series\_matrix.txt.gz")) download.file(paste(url, filenm, sep=""), des…

limma beadarray illumina

updated 6.8 years ago • 261092095

objects being input, what is the best way to coerce to a `data.frame`? I would like to keep column names in the current gene symbol format. They might have unusual symbols like HLA-A, for example. `as.data.frame` automatically...converts column names to by syntactically valid, by doing things such as replancing hyphens by periods. `data.frame(myDataFrame, check.names

S4Vectors

updated 3.9 years ago • Dario Strbenac

two conditions, I tried cont.VEGF <- makeContrasts(contrasts="cond0:timePoints- cond1:timePoints",levels=design) fit2 <- contrasts.fit(fit, cont.VEGF) fit2 <- ebayes(fit2) topTable(fit2) but I seem to have the wrong contrast...following error: Error in makeContrasts(contrasts = "cond0:timePoints- cond1:timePoints", : The levels must by syntactically valid names in R, se…

updated 10.7 years ago • Linus Schumacher

there a maximum number of files that I can import using tximport? I'm receiving the error where the names must be the same length as the vector. I have looked at the other responses, and none have helped so far. Thank you. Laurie

r

updated 5.0 years ago • laurie.r.gray

I . get this error   \`Error in getBM(attributes = c("UniProtKB/Swiss-Prot", "UniProtKB Gene Name",  :    Invalid attribute(s): UniProtKB/Swiss-Prot, UniProtKB Gene Name  Please use the function 'listAttributes...to get valid attribute names\` &nbsp

r biomart

updated 7.7 years ago • al14

across a specific question several times: Which cdf is the most common/complete/appropriate for gene level arrays? I know that the one-to-one mapping of probes to probesets is not valid any more for these arrays. Hence you will lose...which offers completely redefined probesets but again you will lose many probes. I think there must be people around, who analyze these arrays quite frequently an…

cdf xps cdf xps

updated 15.1 years ago • Stefanie Tauber

I have a strange error when I call ChIPQC. > 'names' attribute [9] must be the same length as the vector [2] Number in brackets vary depending on the number of samples. RNFC81...Computing metrics for 9 samples... list Bam file has 194 contigs Error in names(res) <- nms : 'names' attribute [9] must be the same length as the vector [2] Calls: …

chipqc

updated 4.2 years ago • ZheFrench

paste(aType, "-", paste("(", paste(setdiff(allTypes, aType), collapse = '+': Non-valid names: sampleIDOSCC_12-P,sampleIDOSCC_12-R1,sampleIDOSCC_16-P,sampleIDOSCC_16-M etc

limma

updated 8 months ago • Dario Strbenac

Error in setTrackXscaleParam(trackList[[1]], attr = "position", value = list(x = 122929700, : attr must be a slot name of xscale object 3. stop("attr must be a slot name of xscale object") 2. setTrackXscaleParam(trackList[[1]], attr

trackViewer

updated 5.3 years ago • liruiradiant

without problems in easyRNAseq and GenomicAlignments. But now I get. The bam files are seemingly valid and can be accessed by samtools, but the header contains few duplicated entries. reads = readGAlignments('test.fastq.gz.clipped_M.bam.sorted.bam...in GAlignments(seqnames = bamcols$rname, pos = bamcols$pos, cigar = bamcols$cigar, : 'seqlengths' must be an integer vector with uniqu…

software error easyrnaseq genomicalignments bam

updated 9.5 years ago • Michael Dondrup

to run MAST on a subset of single cell types, but I get the following error: Error: grouping factors must have > 1 sampled level Grouping factors are: ``` group ngeneson replicate neuroblastoma.Bridge -0.791254569558456 jansky...jansky neuroblastoma.Bridge -0.588197072041079 jansky ``` et. cetera, with more than 1 level for each. ```r find_de_MAST_RE <- function(adata_){ # c…

Mast mastR MAST

updated 13 months ago • Andrew

very low p-values from just two biological replicates > > doesn't lead you to question the validity of the p-values?? :) > >But we don't just have two biological replicates. We're interested in >consistent gene expression...independent. > We made two biological replicates >of each line, and the expression level of each gene was estimated by 14 &…

probe probe

updated 21.5 years ago • Gordon Smyth

7 x 7 in image Using Sample as id variables Saving 7 x 7 in image Saving 7 x 7 in image Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", : 'names' attribute [9] must be the same length as the vector [7] In addition: Warning message

software error

updated 5.1 years ago • sonyuna90

ranges = IRanges(start = 1:2, end = 4:5)) ``` I want to change the chromosome names all to "chrX" ``` > seqnames(gr) <- "chrX" Error in .normalize_seqnames_replacement_value(value, x) : levels of supplied 'seqnames...must be identical to 'seqlevels(x)' ``` Please let me know if there is a simple way to do this. Best regards

genomicrang GenomicRanges

updated 3.4 years ago • changxu.fan

MakingNewOrganismPackages.htm This are the dataframes and the commands I used: > test3 GID Gene Name Protein Name 1 PSE\_0724 PSE\_0724 GCN5-related N-acetyltransferase 2 PSE\_0725 PSE\_0725 GCN5-related N-acetyltransferase...in evaluating the argument 'x' in selecting a method for function 'unique': Error in structure(res, levels = lv, names = nm, class = "factor") : 'names' attribute…

annotationforge Annotation GO

updated 10.6 years ago • artur

t", row.names = FALSE) files <- file.path(dir,"salmon_quant", samples$sample, "quant.sf") names(files) <- samples$sample tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v28.csv")) txi <- tximport(files, type="salmon...getting is: ``` reading in files with read_tsv 1 2 3 4 5 6 7 8 9 10 11 12 13 Error in attr(x, "names") <- as.character(value) :…

software error RNAseq tximport R

updated 5.7 years ago • caranlove

pre> x <- findChromPeaks(raw, param = cwp) Error in names(res) <- nms : 'names' attribute [12] must be the same length as the vector [6]</pre> I don't understand the error above. I can't seem to

R xcms vector

updated 7.5 years ago • bhgyu

I am trying to use the PAPi package but I get the same error all the time:  <pre> 'names' attribute [1] must be the same length as the vector [0] In addition: Warning messages: 1: In if (getpath != 0) { : the condition has length...Below is the head() of the data and below that is the papi() function. PLEASE HELP!!!!!!! <pre> Names Sample1 Sample2 Sample3…

PAPi metabolomics pathway analysis raphael

updated 6.7 years ago • maryke.wijma

sample' (mc.cores = 32, mc.preschedule = FALSE) [BSmooth] smoothing done in 17656.1 sec Error in names(object) <- nm : 'names' attribute [25] must be the same length as the vector [2]</pre> Here is the session info: <pre> > sessionInfo

bsseq bsmooth

updated 7.5 years ago • ravi.tharakan

Sorry for the delay. On 01/19/2012 07:33 AM, Yuval Itan wrote: > Dear Herve, > > My name is Yuval, I am a postdoc at the Rockefeller University. I am trying to use Bioconductor for analyzing my RNA-seq data, and...I would be grateful for your advice as my R level is a bit basic and I got stuck. I need to count the number of reads per gene and my fastq data was aligned to chr…

Cancer TranscriptDb convert Cancer TranscriptDb convert

updated 13.2 years ago • Hervé Pagès

__Edit__: One of my bam files has size 0 on disk! I get the following error when I call summarizeOverlpas:   <code>Error in names(res) <- nms :<br/>   'names' attribute [15] must be the same length as the vector [2]<br/> Calls: summarizeOverlaps ... .dispatchBamFiles -> bplapply -> bplapply -> bplapply -> bplapply<br/&…

software error summarizeoverlaps biocParallel

updated 8.6 years ago • chriad

kg.mouse = kegg.gsets("mouse")</pre>   I get the following error:   <pre> Error in names(kg.sets) = paste(species, ks.names, sep = "") :    'names' attribute [1] must be the same length as the vector [0] </pre> or   <pre

gage pathview

updated 9.5 years ago • martin.hoelzer

of missing data ..calculating observed preservation values Error in make.unique(rownames(datRef)) : 'names' must be a character vector ``` Here is a reproducible example with a fake dataset: library(WGCNA) setLabels = c("one", "two"); multiExpr

R WGCNA

updated 5.9 years ago • Alex Nesmelov

When trying to use ATACseqQC on a larger bamfile, I receive the following error: **Error in .local(x, ...) : strand values must be in '+' '-' '*' Calls: splitGAlignmentsByCut ... normalize_strand_replacement_value -> strand -> strand -> .local** I checked the structure of the bamfile using **str(gal)** and under strand values I see: **Factor w/ 3 levels "+","-","*": 3…

ATACseqQC R

updated 5.7 years ago • mbasam

gt; varPart <- fitExtractVarPartModel(Filt_EXP1, form, clin) Error: number of levels of each grouping factor must be < number of observations > form <- ~ (0|submitter_id) > varPart <- fitExtractVarPartModel...Filt_EXP1, form, clin) Error in (function (cl, name, valueClass) : assignment of an object of class “numeric” is …

variance formula expression

updated 6.2 years ago • rina

div class="preformatted">Hi everyone, Does anybody know a way to work with bead-level Illumina SNP data ? I'm interested in the correction of potential spatial bias on Illumina SNP arrays, especially the...idat files), but here I need to process the data in a different way : the correction on spatial bias must take place on the images of the array, i.e on bead-level data (.txt or .TIFF files…

SNP Normalization GO PROcess beadarraySNP SNP Normalization GO PROcess beadarraySNP

updated 15.0 years ago • Jonas Mandel

nbsp;      mode = "onDisk")   > mzs <- mz(raw\_data) Error in names(res) <- nms :    'names' attribute \[50\] must be the same length as the vector \[25\] In addition: Warning message: stop worker

xcms xcms3 mzxml

updated 6.6 years ago • goh

I am running multi-level experiment of a dataset using LIMMA, contrast\_matrix\_Grade<- makeContrasts(AdvanceVsEarlyinT = A.T-nA.T,   &nbsp...nbsp;                           levels = design\_Grade) fit <- eBayes(contrasts.fit(lmFit(eset,design = desi…

topgo

updated 7.5 years ago • peirinl

chipqc) ``` When I ran the function ChIPQC, I got the following error: ``` "Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", : 'names' attribute [9] must be the same length as the vector [7]" ``` I continued to run the ChIPQCreport

ChIPQC

updated 5.8 years ago • analeigh.gui

<div class="preformatted">Hi Everyone, I was really hoping someone could help me with this; I've tried searching to no avail, however I apologise if something similar has been discussed before. I'm trying to use crlmm to carry out LOH and CNV analysis based on .idat files created using the Illumina 1M bead chips. I'm sure I've got it installed correctly (I'm new to Bioconductor, but I've…

crlmm crlmm

updated 12.8 years ago • Richard Thompson

<div class="preformatted">Hi, Given a dataset for Affymetrix arrays normalized with mas5 or rma we usually made the experience that signals below 80 (6,3 in log2 format) are hard to validate with PCR. Can somebody tell me, how I can judge on dChip normalized data in a analog way? Where can I draw a threshold to...mas5 or rma we usually made the experience that signals below 80 (6,3 in log…

updated 16.6 years ago • Benjamin Otto

<div class="preformatted">Dear Paolo, Cross validation in what context? If you are looking for cross validation for microarray studies, a quick search on Current Index to Statistics (www.statindex.org) turned up only one article: Raghavan, Nandini, Amaratunga, Dhammika, Nie, Alex Y. and McMillian, Michael (2005) Class prediction in toxicogenomics Journal of Biopharmaceutical Statistics, …

Microarray Microarray

updated 19.0 years ago • McGee, Monnie

genome information (try:0) Using: Homo sapiens genes (GRCh37.p13) Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column</pre> Here is my code that I want to use to download and prepare the expression data of the

TCGA tcgabiolinks Error

updated 7.8 years ago • f.geist

before eBayes: fit <- lmFit(E, design = design) contr <- makeContrasts( A-B, C-B, A-C, levels=design) fit <- contrasts.fit(fit, contrasts = contr) nc <- fit\[grepl("antisense|non-coding|pseudogene|vault|non-protein...nc.eb <- eBayes(nc) write.fit(nc.eb, adjust = "BH", file="fit.nc.txt") Is this valid? If not, how would you proceed. Thank you for y…

limma genefilter

updated 8.8 years ago • minabashir

of validating our systems and software. I was wondering has anyone gone through the process of validation with R and if so could you point me to any resources that may help show how this should be done? Thanks Elliott </div

PROcess PROcess

updated 14.4 years ago • elliot harrison

ExpressionSet (storageMode: lockedEnvironment) assayData: 20172 features, 60 samples element names: exprs, se.exprs protocolData sampleNames: GSM330151.CEL GSM330153.CEL ... GSM331677.CEL (60 total) varLabels: ScanDate...parameters have been calculated and checked. Building classifier... 11:12:02 - 1 out of 5 cross-validation loops finished. 11:12:40 - 2 out of 5 cross-…

software error geNetClassifier

updated 8.5 years ago • polemiraza

DESeq2 to compare gene expression by condition across multiple brain regions. "condition" has 2 levels. "region" has 7 levels. I have n=3 treatment and n=3 control in each region for a total of 42 samples My goal is to compare gene...that "condition_B_vs_A" will return the results describing the effect of condition in the first level of region (so, the effect of condition in region A). Th…

DESeq2

updated 3.0 years ago • EJB

div class="preformatted">Hi, all, I want to randomly shuffle sample names in an object of expressionSet, aiming to perform permutation test. I did as follows, but the following test result remained...unchanged (When I shuffled the original data file names before 'ReadAffy()' , the result did change). So it must be wrong; what's the way please? Thanks to everybody who help / has helped...filen…

updated 16.4 years ago • Al Tango

history (`colData$history`, below) but want to better test the accuracy of the results with cross-validation, by sampling from the control group without replacement. Is there a clean way to do this with limma? ``` C.H <- as.factor...condition = (C.Hcondition.TRUE + C.Hcondition.FALSE) - (C.Hcontrol.TRUE + C.Hcontrol.FALSE), #2 levels=design) fit2 <- contrasts.fit(fit…

limma

updated 3 months ago • Ali Barry

Hi, I am trying to convert gene names to enterz ids for further analysis. I am using: BiocManager::install("AnnotationHub") library(AnnotationHub) hub <- AnnotationHub...I got an error: Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'GENENAME'. Please use the keys method to see a listing of valid arguments. Thank you

Bioconductor

updated 2.4 years ago • gk13102603

don't have mismatch probes, therefore MAS5 cannot be used. According to Affymetrix, the DABG is not valid on gene level: "There is a strong assumption in DABG that all the probes are measuring the same thing (i.e., the same transcript...This is not the case at the gene level due to alternative splicing. For example, probes for a cassette exon that is skipped will contribute to a mis- leadingly.…

probe xps probe xps

updated 14.6 years ago • Pascal Gellert

Thanks for the bug report. This is fixed in IRanges 1.17.11. Note that the data inside the rle must be a factor. Adding levels to an Rle after the fact doesn't create a factor-Rle. x = Rle(c(2,3,1,2,3,2),rep(2,6)) levels(x) = as.character...0:5) This is a numeric-Rle with no levels. > x numeric-Rle of length 12 with 6 runs Lengths: 2 2 2 2 2 2 Values : 2 3 1 2 3 2 > tab…

IRanges IRanges

updated 12.4 years ago • Valerie Obenchain

did. > pg=topTable(ebFit, coef=1, number=1000, p.value=0.05, lfc=1) > de_pg <- pg[,5]> names(de_pg)<-pg[,3] de_pg is a numerical vector of log2 fold changes, with EntrezIDs as names, as DE_Colorectal, the example dataset...14825 5.189596 > is.vector(DE_Colorectal)[1] TRUE> DE_Colorectal[1] 3491 5.960206 The names of de_pg are in all, simila…

Organism limma SPIA Organism limma SPIA

updated 13.3 years ago • Moritz Kebschull

Hi, thank you for your work! I am a bit confused as to obtaining the spot vs cell level data. Following the [spatialLIBD documentation][1], under the Processed Data section, to download spot-level data, one must...call `spe`: ```r ## Download the spot-level data spe <- fetch_data(type = "spe") ## This is a SpatialExperiment object spe ``` However, from a second [documentation page][2...…

spatialLIBD

updated 2.7 years ago • kstern

div class="preformatted">Did anyone know how to do the k-fold validation on the training data set by SVM? Thanks. Guangchun </div

updated 22.2 years ago • Song, Guangchun

raw) exprs(rawSub) <- es Error in assayDataElementReplace(object, "exprs", value, validate = TRUE) : unused argument (validate = TRUE)</pre> In the current Bioconductor version (3.4) the function "assayDataElementReplace...indeed does not have an argument "validate". In previous versions this function had "validate" as an argument, and the default was TRUE. My guess is tha…

HTqPCR

updated 8.2 years ago • henrik.seidel

pre> ------------- return: <pre> Error in extractROWS(x, i) : Problem(s) found when testing validity of SortedByQueryHits object returned by subsetting operation: 'queryHits(x)' must be sorted. Make sure to use a subscript...that results in a valid SortedByQueryHits object. > sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bi…

summarizeOverlaps genomicalignments

updated 8.6 years ago • philipp.wahle

biological results. my experiment is biologically replicated on FEBIT arrays, and i want to validate my results with it. Now I'm working with the same statistical test, and clustering algorths. now, how would you suggest

Clustering Clustering

updated 19.7 years ago • claudio.is@libero.it

background-color:Yellow">Error in makeS4FromList("BSgenomeDataPkgSeed", x) :    some names in 'x' are not valid BSgenomeDataPkgSeed slots (SrcDataFiles)</span> I'd appreciate  help to understand what's wrong

bsgenome

updated 10.3 years ago • qiwang1993

div class="preformatted">Hi all, I'm looking for some reference paper about cross validation. Could you, please, suggest some 'state of the art' reviews et similia? Sincerely, Paolo </div

updated 19.0 years ago • portnoy@supereva.it

RNAseq data analysis to identify differentially expressed genes (DEG) using DESeq2. I am trying to validate the results of my pipeline with previously published experiments but I dont seem to find any papers using the current...can generate significantly different results. ¿Does anyone know of a dataset that I can use to validate my pipeline with v1.30.0 of DESeq2? Thanks

DESeq2

updated 4.2 years ago • Samuel Daniel

for enrichment of terms directly annotated by a given gene. I would like to be able to customize the level of abstraction of my analysis such that I can ask questions about higher level GO terms, which I'm hoping will increase...for specific questions by reducing the amount of multiple hypothesis testing correction that I must implement. Does anyone have insight on the best way to approach this

gene ontology GO overrepresentation analysis missmethyl gostats

updated 8.7 years ago • graggsd

Hi,   After doing DESeq2 with RNA seq data, the output I obtain is an excel file with ensembl transcript ID, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj. I would like to know 2 things: -If you know if there is any code that I can use in order to obtain the gene name or description in the output file instead of the ensembl transcript ID -If there is any code to obtain mor…

deseq2 gene columns output

updated 9.4 years ago • amyfm

Dear all, I have a problem with the PSICQUIC package while mapping gene name synonyms. Here are the command lines : \# data fetching tbl.big <- PSICQUIC::interactions(psicquic, species="9606",provider...attribute(s): uniprot\_swissprot\_accession  Please use the function 'listAttributes' to get valid attribute names   I cannot figure out what had changed, since this…

psicquic

updated 9.9 years ago • anais.baudot

about combining the three files into a single one is that I'm not able to set ylims for each of the levels of the variable. This is an example of one of my input files (the one containing the SNP info): <pre> chr10 47000019 47000019...This function loads a BED-like file and stores it as a GRanges object. # The tab-delimited file must be ordered as 'chr', 'start', 'end', 'id', 'sco…

ggbio ggplot2 legend bioconductor karyiogram

updated 8.6 years ago • oswaldo.lorenzo