Bioconductor Forum

https://genome.ucsc.edu/cgi-bin/&quot">https://genome.ucsc.edu/cgi-bin/&quot</a>;) Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) : 'names' attribute [210] must be the same length as the vector [209]</pre> Indeed if I tried to list the...message <pre> supportedUCSCtables(genome="hg19", url="http://genome.ucsc.edu/cgi-bin/") Error i…

software error genomicfeatures

updated 7.6 years ago • rmendez

2013-02-24 23:17:38 -0800 (Sun, 24 Feb 2013) | 3 lines Tweak to GRanges() constructor so the names of the supplied metadata cols don't run in conflict with some obscure internal argument names. ---------------------------------------------------------------------- -- Means that we can no longer...mycol <- 1 GRanges("chr1", IRanges(1, 10), "+", mycol) And get a GRanges with a metadata c…

updated 12.7 years ago • Michael Lawrence

on a DNAStringSet, i.e., >> what is your use case? >> >> >> unique() on a named character vector drops names: >> chr <- c(a="A", c="C", aa="A", c="CC") >> > unique(chr) >> [1] "A" "C" "CC" >> >> >> Same for a named list...1] "CC" >&…

Cancer Cancer

updated 13.0 years ago • Hervé Pagès

I am doing this work was keen to have a heatmap of the differentially expressed genes expression levels. Unfortunately, the design is rather complex and random (closer to a loop design than a common reference) so its not possible...show that the expression of the two groups are different? In particular I was thinking that there must be estimates of the expression and error in each group by the …

Microarray Cancer limma Microarray Cancer limma

updated 17.1 years ago • Daniel Brewer

bioc-issue-bot: ---- Dear @... You (or someone) has already posted a repository with the same name to our tracker. See https://github.com/Bioconductor/Contributions/issues/ You cannot post the same repository more than...once and packages are not allowed to have the same name. If you would like this repository to be linked to issue number: 2675, Please contact a Bioconductor Cor…

Bioconductor

updated 3.5 years ago • Daan

Z70218" "L17328" "S81916" "U63332" "M77235" and I would like to find ( in a repository for ex.) the names as: [1] "hypothetical protein LOC221823" [2] "meningioma (disrupted in balanced translocation) 1" [3] "fasciculation and elongation...to extract almost everything, from locuslink to PMID to FASTA sequences, but the Descriptions (or names)... I've looked in the web and the vignettes of cours…

annotate annotate

updated 19.7 years ago • Giulio Di Giovanni

HMM routine, I have data showing chromosome number and nucleotide position, but no associated gene name or database identifier. e.g. > logRiList[[1]][1:10,] chromosome position end logR state 1 1 10004 10004 0.7627 3 2 1 46844 46844...3 How can I map this data to RefSeq Accession number or EntrezGene ID etc. so I can get the name of the gene asso…

Cancer Breast Cancer Breast

updated 16.6 years ago • Steven McKinney

Symbol or Entrez ID in R? I am using `AnnotationDbi` and org.Hs.eg.db but it seems to give old gene name. For entrez ID 64755, the new gene name is [RUSF1][1] but it gives C16orf58 ```r library(AnnotationDbi) library(org.Hs.eg.db) AnnotationDbi

AnnotationDbi org.Hs.eg.db

updated 4.7 years ago • sgupt46

corrected gene count estimates. The tximport vignette provides two methods for importing gene-level counts for DGE (differential gene expression), namely: Namely, the “original counts and offset” method and the “bias corrected...argument > countsFromAbundance="lengthScaledTPM" or "scaledTPM", and then to use > the gene-level count matrix txi$counts directly as you would a r…

tximport deseq2

updated 6.8 years ago • Thomas Bradley

GRanges( seqnames = Rle(chr), ranges = IRanges(start, end=end, names=rsid), strand = Rle(strand("*")) ) ) loc_all <- locateVariants(target, txdb, AllVariants(intergenic=IntergenicVariants(50000...50000))) names(loc_all) <- NULL out <- as.data.frame(loc_all) out$names <- names(target…

annotation variantannotation rstudio

updated 9.7 years ago • noor.suaini

0 rows into table bgfeature... Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions 1. Make sure you the probes which are labeled +ACI-experimental+ACI- are not the ones with no sequences...0 rows into table bgfeature... Error in sqliteExecStatement(con, statement, bind.data) : bind.data must have non-zero dimensions Best, Nitesh +AFsAW…

Annotation probe Annotation probe

updated 12.2 years ago • Nitesh Turaga

Is there a way to map Uniprot names (e.g. RASH\_HUMAN) to other identifiers using Bioconductor? I have tried biomaRt, the AnnotationDbi-based packages

uniprot.ws

updated 4.7 years ago • Diego Diez

nbsp; Both are fitting the same model (`` ~ GROUP) ``, where group is a factor with four levels, and specifying a contrast in `` results  ``using the names of the variable and factor levels (contrast = c("GROUP", "A

deseq2 modelMatrixType DESeq

updated 10.0 years ago • Gregory Warnes

I can't run a Bayes fit on this data. I have some NA's in my data set that does not fit within the levels MU or WT, could this be what's going wrong? and if so can anyone suggest any ideas? Many thanks! ```r treatment <- factor(clinical...treatment, levels=c("MU", "WT")) #clinical is a csv file which cointains details of the microarray (including file names and treatment) design

limma

updated 4.9 years ago • d808bc07

bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.gz': status was 'Couldn't resolve proxy name'URL 'https...bioconductor.org/packages/3.11/bioc/src/contrib/PACKAGES.rds': status was 'Couldn't resolve proxy name'URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/PACK…

bioconductor installation proxy BiocManager

updated 5.5 years ago • chen

uses gtf file "gene_id" by default, in the result count table, I have a very big list of MSTRG------ named genes. I would like to know if using an option in featureCount gives the posibility to change from gene_id to ref_gene_id...Would this change be correct? Or maybe I have realized now that there is another option named −−extraAttributes < string > (GTF.attrType.extra) and I can…

featureCount rna-seq gene_id re_gene_id stringtie

updated 6.9 years ago • IRAIA.MAIALEN

using ClusterProfiler. However, I'm facing a problem that I'm unable to convert the ENSEMBL gene names to ENTREZ ID. Can you please help me with that? Below all information about the code and Error I'm getting. Code should be...ENTREZID") Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing o…

clusterProfiler

updated 3.5 years ago • martacrespi7

pseudocount, labels, smooth, ...) :    One or more values of 'x' or 'y' are not valid sample names!   Here is the sessionInfo()   R version 3.4.3 (2017-11-30) Platform: x86\_64-apple-darwin15.6.0 (64-bit

cummerbund

updated 7.8 years ago • seyfim

are retained (see sample below) DNAMultipleAlignment with 8 rows and 2343 columns aln names [1] ###ATGGTACAGGG############...######################### Human [2] ###ATGGTACA---############...######################### Chimp [3] ###ATGGTACA---###########...######################### Cow [4] ###AT----CAGGG##########...######################### Mouse Is there a way to…

biostrings

updated 5.6 years ago • multipleseqs

in biomaRt. The following arrays: HumanWG6_V1, HumanRef8_V1, MouseWG6_V1, MouseWG6_V1_B do not have valid Illumina probe names under the "ProbeId" column. They seem to contain values which are in the column "Array_Address_Id

Annotation probe biomaRt Annotation probe biomaRt

updated 16.8 years ago • Nenad Bartonicek

with between group analysis (BGA) from the made4 package and I have a problem with some of the affy names: I tried bga.suppl(training.set[list,], supdata=test.set[list,], classvec=cl_train, supvec=cl_test) 'training.set' and 'test.set

Classification affy made4 Classification affy made4

updated 19.0 years ago • Heike Pospisil

here one book written by Michael one of the authors of `DESeq2` I get the following from this book named Data Analysis for The Life Sciences. ```r X<-model.matrix(~type+leg, data=spider) colnames(X) "(Intercept)" "typepush" "legL2""legL3...legL4" ``` So here they point out a model with one factor `type` with two level `push` and `pull` and another factor `leg` with 4 levels `leg1` `…

DESeq2

updated 4.4 years ago • Alexandre

to apply SVA to a matrix that's 164K x 51. There are two variables of interest: sample tissue (2 levels) and age (6 levels). # xpr is my matrix of microarray intensities modmat <- model.matrix(~1 + as.numeric(pheno$tissue), xpr) # result...15 Iteration (out of 5 ): Error in cbind(mod0, uu$vectors[, 1:n.sv]) : number of rows of matrices must match (see arg 2) ---- Is SVA inappr…

Microarray sva Microarray sva

updated 12.7 years ago • Shraddha Pai

by breaking your learning set (samples with know classes) into training and test set. Look up "cross validation". Some example of built in cross validation * knn.cv() is a leave one out cross-validation of knn() * svm() in library(e1071...has an argument named 'cross' for cross validation In practice, I prefer to write my own wrapper for cross-validation to ensure that sampling

Microarray Clustering Category Microarray Clustering Category

updated 21.4 years ago • Liu, Xin

<div class="preformatted">Hello, I created a filter function to filter the microarray data set by row variance, but got follow error: > dim(data1) [1] 7129 38 > data1[1,2:4] data[, 4] data[, 6] data[, 8] 1 -139 -76 -135 > myfilter<-function(j){ + function(x){ + rowVars(x)<j +="" }=""> > ff<-filterfun(myfilter(2…

Microarray Microarray

updated 16.7 years ago • wxu@msi.umn.edu

Invalid attribute(s): SYMBOL, SYMBOL Please use the function 'listAttributes' to get valid attribute names** I understand that it is for SYMBOL, but I don't know which one is correct. My identifiers are like this: Zm00001eb002010...diff_genes <- read_delim(file = "UP_lgn_vs_WT_filtrado_estricto.csv", delim = ",") # Assign names to the first column colnames(diff_genes)[1] &lt…

biomaRt clusterProfiler Zea_mays

updated 22 months ago • sanchezsanchez

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 9.5 years ago • emily.mccann

I am using Fedora35 to study expression level analysis. I want to load the following file (Sample2condition.txt) with tximport. ![enter image description here][1] So...I am using Fedora35 to study expression level analysis. I want to load the following file (Sample2condition.txt) with tximport. ![enter image description here][1] So, I...stringsAsFactors=F) $ s2c$group &…

Linux R tximport

updated 3.8 years ago • nakane_clan

now I want to visualize the results. I want to graph heatplots and cnetplots but reading the genes names/symbols instead their ENSEMBL ID's. Is this possible? If yes, how

clusterProfiler enrichplot

updated 2.7 years ago • GenoMexa

<div class="preformatted">Hi, I am very new to bioconductor and microarray analysis in general. I am using Windows XP and R version 2.5.1. I have a few questions about the limma package that I am using for cDNA array analysis. First: I would like to flag out all spots with fluorescence intensity lower than that of the mean background intensity of the array. The weight function I am using …

Microarray Normalization limma Microarray Normalization limma

updated 18.2 years ago • Brooke LaFlamme

oligo for my analysis, and managed to get results of differential expression both at the transcript level and at the probeset level. The reason why I thought oligo wasn't appropriate was that it can't do transcript-level presence...this strain. Hence I thought it was important to do the presence / absence calls at the transcript level. I believe a transcript-level analysis is best suited for ge…

microarray oligo gene ST pacalls

updated 8.6 years ago • Sophie Marion de Proce

experiment)</pre> with the error message: Saving 7 x 7 in image Error: Faceting variables must have at least one value The traceback is: 10: stop("Faceting variables must have at least one value", call. = FALSE) 9: layout\_base

ChipQC chipqc

updated 9.2 years ago • thekatybrown

not running the same code for a month or so, I am getting a new error. I am now getting NAs as probe names for datasets using getGEO(). It seems that datasets obtained with platform GPL4372 are having issues but platform GPL2700...GSEMatrix =TRUE, AnnotGPL=TRUE) if (length(gset) > 1) idx <- grep("GPL4372", attr(gset, "names")) else idx <- 1 gset <- gset[[idx]] fData(gs…

GEOquery

updated 3.9 years ago • John

Hello, All the codes are running well. I tried to plot the enrichment of the GSEA. But it comes out the error. Thank you in advance for great help! Best, Yue > library(fgsea) > library(tidyverse) > library(data.table) > library(ggplot2) > setwd("/media/hp/04c65089-71ff-4b33-9a30-c21b8c77eda2/li/HASM_SILAC/finally/DEP") > …

fgsea

updated 4.8 years ago • yueli7

perform differential expression analysis. My design has a single factor, diagnosis, which is a multi-level factor with six different diagnoses: 'Craniopharyngioma', 'ATRT', 'Ependymoma', 'Glioblastoma', 'Glioma', and 'Medulloblastoma...the results() function without specifying any contrast, I get comparisons with 'ATRT' as the base level, as seen in the names of the coefficients from resultsNames…

DESeq2

updated 2.5 years ago • Amdom

<div class="preformatted">Hi everybody, I have a problem working with GO annotations. I would like to group my data according to their GO categories, but only of one level. I have a data.frame (three columns: WT, mutation, mean(WT/mutation) and ca. 3150 rows) row.names mut WT WT_mut 1737_Sepsecs 0.6924728 0.00728067 95.111137 1478_Ube2m 4.6102070 0.11428570 40.33…

Annotation GO Annotation GO

updated 14.7 years ago • Assa Yeroslaviz

for feature names, correct? I hope the following is clear but if you need more info or context please let me know. Thank you! >raw <- readCtData...48 features, 44 samples Feature types:           Feature names:         PD1 BCL6 BATF ... Feature classes:&…

limma ndups htqpcr software error

updated 10.3 years ago • julio.c.silver

across all samples to represent the expression of that gene. As I am trying to change from probe-set level to gene level analysis I was hoping that there must be some function already to do this in 'affy' or 'limma'. @Martin: I think...gene. This way I want to remove the redundancy by keeping the analysis >> to single gene entry level. I am fully aware that it is not a nice thing &…

GO probe Biobase genefilter GO probe Biobase genefilter

updated 12.7 years ago • Atul Kakrana

however biomart ensembl hgnz\_names only contain 19869 out of my 29581 genes. In my dataset, gene names are HUGO, too. It seems that around 10,000 of my genes are not included in the total of 36,713 genes in biomart ensembl. I checked...to see if there is a potential naming difference, but I couldn't find anything incriminating. Does anyone have an idea why that happens? Thanks

biomart ensemblbiomart

updated 8.2 years ago • spr

data (in my case Agilent) be used to get a measure of: (a) absolute (approximate) expression level (say E) of a gene/probe (b) can the Es for a gene/probe from two or more control samples be compared to get an idea of the general

updated 14.5 years ago • Hari Easwaran

neurooncolab new pc/Documents/R/win-library/2.10/hugene10stv1.r3cdf. Before using this package it must be installed via 'R CMD INSTALL' at a terminal prompt (or DOS command shell). If you are using Windows, you will need to get set...library(hugene10stv1.r3cdf) Error in library(hugene10stv1.r3cdf) : 'hugene10stv1.r3cdf' is not a valid installed package * *>* I have tried google, but can…

cdf probe cdf probe

updated 15.9 years ago • sneha patil

PM To: r-help Cc: bioconductor Subject: [BioC] colnames and get means for the columns with the "same" names hi, I have a conversion table for colnames like this: Probe_ID HUMAN_LLID 1 AF106325_PROBE1 7052 2 NM_019386_PROBE1...colnames to another ID's system, HUMAN_LLID by using the table. The colnames of x1 with the same names (in HUMAN_LLID) need to be averaged. Is there a good…

convert convert

updated 19.1 years ago • Sean Davis

Hello, I am using DESeq2 to perform LRT analysis. I have 4 conditions, and each group named Group1, Group2, Group3, and Group4. Each group has 80 to 100 samples. I use only p-adj value to determine DEGs. Whenever I use...function, the last group (like group4) has distinctive characteristics. When I changed the group name (group3 to group4, group4 to group3), DEGs were changed. (common DE…

deseq2

updated 6.1 years ago • minyoungcho93

Hi, I have 6 text files contain chromosome's  name, start, and end and probe's name and CpG numbers. I want to read these files in R and then do some processes with this data. Used...Chr.txt",header=TRUE, sep="\\t") d=as.numeric(my\_data\[1,1\]) > my\_data\[1,1\] \[1\] 13 Levels: 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9 X Y > d \[1\] 5 Th…

warning text read.delim

updated 8.4 years ago • niutster

I just installed monocle package to analyze some data. When I ran the example in package which names "HSMM\_analysis.R" to learn to use monocle, Rscript reported a bug: <pre> Error in argfun(start + i - 1L) : no slot of name "expressionFamily

monocle bugs

updated 10.1 years ago • wanghao1993333

pca, tSNE=tsne) )</pre>   The error message is <pre> Error in checkSlotAssignment(object, name, value) : assignment of an object of class “GRangesList” is not valid for slot ‘rowRanges’ in an object of class “SingleCellExperiment

singlecellexperiment

updated 8.1 years ago • Shian Su

exon, then you can use DexSeq to calculate differential exon usage. If you want to calculate gene level differential expression, then you count per transcript, and the use DESeq/2 to calculate differential expression...I am interested in gene level differential expression (at this point), I subsetted my gtf file for the CDS, where CDS is found in the 'type' column (gtf reproduced...below). Thi…

GenomicRanges DESeq2 GenomicRanges DESeq2

updated 12.5 years ago • Sam McInturf

method for function 'which': Error in rowSums(BS.cov[, bsseq.data$Type == "SSA-"] >= 2) : 'x' must be an array of at least two dimensions</pre> When I look at the number of CpGs that are covered by at least 1 read in all samples...Warning messages: 1: In .Seqinfo.mergexy(x, y) : Each of the 2 combined objects has sequence levels not in the other: - in 'x': chrX - in 'y…

methylation DMR analysis

updated 10.7 years ago • parker

design is therefore: f = paste(dge$samples$sex, dge$samples$condition, sep = ".") f = factor(f, levels = c("Male.pre", "Male.post", "Female.pre", "Female.post")) d = model.matrix(~ 0 + f + age + dm + axc, colData) cont = makeContrasts(M.PvP="fMale.post...F.PvP="fFemale.post-fFemale.pre", sexDiff="(fFemale.post-fFemale.pre) - (fMale.post-fMale.pre)", levels = d) where colData is my list of …

limma limma-voom limma paired analysis limma contrast matrix

updated 8.7 years ago • gregory.l.stone

FPKM FPKM FPKM ... I understand that DESeq must first normalize the expression values of each treatment by dividing each column with it's own size factor... however, when...without any replicates (Section 3.3 of your guide), in spite of this problem, but I read that one must assume gene expression levels are quite similar between treatments (this is not our case)…

DESeq DESeq

updated 13.2 years ago • Andres Eduardo Rodriguez Cubillos

Greetings. I have an experiment exposing cells to temperature and pollutants. Two factors x two levels per factor. Factor 1 is temperature with two levels (cold (reference level) vs hot). Then factor2 is pollution with two levels...no_pollution (reference level) vs pollution). So 4 conditions: cold non polluted (CNP), cold polluted (CP), hot non polluted (HNP), hot polluted (HP). I have hopefully…

DESeq2

updated 11 weeks ago • Michael

Hi everyone, I am completely new to scRNA-seq data analysis and I am trying to figure out how to include only cells that fulfill a certain criterion (in my case only activated T cells, from other cells, based on the expression of an activation marker) I figured that I would have to set a threshold for the expression level of that activation marker in order to sort out the activated cells …

scRNAseq

updated 4.9 years ago • Iris Wing To

simple solution wherein I can convert the .h5 file into an R data frame or data table and have gene names added as a separate columns or as row names. I came up with this solution but wondering if this works? I am assuming here

tidyverse R SingleCellExperiment SingleCellData

updated 2.0 years ago • Sitapriya

Dear Community,   I am reading a single cell file and processing it along with TSNE. Finally generation of loom files.   The commands that I am using to read file is :     <pre> loadSCE <- function(path){ sce <- scater::read10XResults(path) #sce <- normalize(sce) # Data normalization based on scran mitochondrialG…

Scater LoomR SCopeloomR

updated 6.9 years ago • Abhishek Singh

only one treatment to the baseline. My data are the results of RNAseq wherein gene expression level was measured. I have 2 treatments, the baseline called APO, and one treatment called SYM (n=3 for both). I wish to compare the...expression level between the two groups to find genes that are expressed to a significantly higher degree in the SYM treatment than...run the rest of the analysis. …

limma

updated 16 months ago • AL

Warning messages:1: In maximumLevels(fac, n = length(colors)) : A factor was provided with 9 levels, but only the first 9 were used for coloring.2: In maximumLevels(fac, n = length(colors)) : A factor was provided with 9 levels...were used for coloring.3: In maximumLevels(fac, n = length(colors)) : A factor was provided with 9 levels, but only the first 8 were used for coloring. >sp…

Microarray arrayQualityMetrics Microarray arrayQualityMetrics

updated 12.1 years ago • Lisa Cohen

a problem and hope someone can help me: Using this command: " clust=clValid(obj=matrix,nClust=2:8,validation=c("internal", "stability"),metric ="euclidean", method ="average",neighbSize = 10,maxitems =dim(matrix)[1], clMethods = c("fanny...I receive the following messages: Warning messages: 1: In vClusters(mat, clMethods[i], nClust, validation = validation, : fanny unable to find 4 clusters,…

updated 16.7 years ago • Jörg

with the reactome.db package: in version 1.50.0 most of the pathway IDs are not mapped to pathway names: library( reactome.db ) reactome.list <- as.list( reactomePATHID2EXTID ) have.name <- names( reactome.list ) %in% ls( reactomePATHID2NAME...In 3.1.2 with reactome.db 1.50.0 only 1518 of 10373 pathway IDs can be mapped to a pathway name, while in R 3.0.2 with reactome.db ver…

annotation pathways

updated 10.7 years ago • Johannes Rainer

<div class="preformatted">hi there, I would like to estimate the effect on gene expression levels of two factors Age and activity (each with 4 levels) using Limma. for my design matrix i have dataB<-data.frame(samples = arrays,Age=factor(FFAge),activity = factor(FFfibrosis)) design<-model.matrix(~activity*Age, data=dataB) (samples contain the names of my arrays) fit &…

limma limma

updated 21.7 years ago • ivan.borozan@utoronto.ca

When using DESeq2 in the past, count data and normalized count data, etc... retained the names of samples indicated in the first column of the colData table. I've used dds = DESeqDataSetFromMatrix(countData..._001 Day1AirDEMED    DEMED         Air     1 I expected the names of the columns in my count matrix from DE…

deseq2

updated 9.5 years ago • jshouse