Bioconductor Forum

I've by now arrived to the end of my analysis, missing only the pathway analysis to contextualize genes with different expression levels. The workflow itself is studied for mouse genes, and suggests, at a point, to import Entrez...Gene Ids from the org.Mm.eg.db package (for mouse) as follows. library(org.Mm.eg.db) y$genes$Symbol <- mapIds(org.Mm.eg.db...analysis anyway, with…

annotation entrez gene ids software error

updated 6.8 years ago • Raito92

Args for manual filtering: ## ## Filtering genes with low expression / zero count. At least 1/nGroup ## ## of the samples have at least min_reads or more reads. Filter base on...design matrix should also ## ## be provided.It's a vector of 0, -1, 1, with names matching ## ## column names…

genefilter edgeR

updated 9.7 years ago • cafelumiere12

Hi, How do I remove the label that is next to the annotation box in the heatmap with ComplexHeatmap ideally I would like to create a block annotation with the name of the sample in it but so far I wasn't able to do it. Also which RGB color is the best to have blue and red and not purple-bluish color in the heatmap? I have 3 samples (ctrl) and 3 treatments. I want the samples in columns and the…

r rnaseq complexHeatmap annotation

updated 5.6 years ago • camillab.

Hello, I want to analyze the differentially expressed genes (DEG) of 3 cell populations between tumor and healthy blood. I have bulk RNA-seq data as a txi matrix containing abundance...counts and length matrixes for 30 samples. I have a metadata file that indicates for each sample: - sample ID - Populations (1,2,3) - Patient (1...3,4,5,6,7,8,9,10) - Tissu (tumor or healthy blood) - batch (seq…

BatchEffect sva DESeq2 RNASeqData limma

updated 2.4 years ago • D-Bug

custom 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...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 16.8 years ago • Steven McKinney

gt; From: Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> > Subject: [BioC] How to check if gene name is an alias or misspelt > To: Bioconductor mailing list <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <49DCAC07.6010804...gt; > Content-Type: text/plain; charset=ISO-8859-1 > > Hello, > > I have a list of genes …

Cancer convert Cancer convert

updated 16.8 years ago • Gordon Smyth

<div class="preformatted">Hello all, Is there anyway to retrieve the gene symbols, full names (discription), or other gene information, given a list of Entrez Gene IDs (or the LocusLink) in Bioconductor. Obviously, one way is to query Entrez Gene web service ID by ID, but is there any way to get connected to that web service from within R/Bioconductor and retrieve the...div class="preformat…

Annotation Annotation

updated 19.6 years ago • Luo Weijun

a matrix of counts. The resulting matrix has 25221 rows and I'm wondering how I can retrieve the gene names for each row.  source("https://bioconductor.org/biocLite.R") biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene...filenames, yieldSize=2000000) txdb=TxDb.Hsapiens.UCSC.hg38.knownGene ebg <- exonsBy(txdb, by="gene") se <- summarizeOverlaps(features=ebg, reads=bamfile…

rnaseq summarizeoverlaps count matrix

updated 8.0 years ago • johnsonn573

column fields that describe the overlap. However if there is an overlap with a gene start, then I want to return the gene start and end locations as well as its chromosome and strand. Any help would be much...genes, x.window) ## maybe limit to only TSS overlaps? # subsetByOverlaps(genes, x.window, type = 'start') signal_window=names(x.window...window_start=window_start, …

iranges R granges

updated 8.4 years ago • ssabri

population-level BCV. As I understand there are three different estimates - a common BCV for all genes, a BCV for each abundance quantile bin and a BCV for each gene based on some middle ground for low-sample-size experiments...variances. Is there a particular scenario and/or option in the package to estimate BCV for each gene directly, e.g., if I have a sample size large enough where this qua…

edgeR

updated 12 months ago • James

div class="preformatted">Is there any general procedure for handling duplicate genes in Affy arrays? For example, for the hu6800 array which has 7129 probe sets, there are 869 genes that are represented by...more than one probe set, with one gene (ACTB) being represented by 9 probe sets. g.symbols=aafSymbol(X.gnames,"hu6800") ug.symbols <- unlist(g.symbols) length...comparison procedu…

hu6800 probe hu6800 probe

updated 20.4 years ago • jsv@stat.ohio-state.edu

some 126 samples using the mouse ensembl reference cDNA transcriptome. Then I tried to obtained  abundance values using tximport as follows: <pre> txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance...lengthScaledTPM", ignoreTxVersion = F) names(txi.salmon) head(txi.salmon$counts) ###Create a matrix of abundance (a.k.a lengthScaled…

tximport deseq2

updated 7.5 years ago • ctl

div class="preformatted">Hi, I was wondering what would be the most efficient strategy to get distances between sequences that belong to two different sets. So far, what I am doing is: library

updated 12.8 years ago • Benilton Carvalho

I'm trying to account for batch effects and variations in quality for a set of samples that were sequenced from at least 5 different research groups. These were sequenced with different read lengths and in my PCA analysis...I'm trying to account for batch effects and variations in quality for a set of samples that were sequenced from at least 5 different research groups. These were sequenced with…

RNASeq DESeq2

updated 3.4 years ago • seeta_rajpara

I have whole exome sequencing data from insect individuals from two different populations. I'm interested to see if there are any genome regions...be any problem, conceptually, with using edgeR for this purpose? They're both dealing with read abundances that vary between individuals and groups of samples. In principle, is calculating differential coverage and...calculating its statistical signifi…

edgeR exome

updated 6.7 years ago • am3

div class="preformatted">Hello, The attached file is the Probe Set IDs related to Human Gene 1.1 ST array. May someone let me know where I could find a .CSV file that includes both Probe Set IDs and gene names for this

probe probe

updated 12.2 years ago • Shahla Ghaumipour

carbon-13 isotopes. I am interested in specifically testing whether a treatment increases the abundance of these minor carbon-13 peaks, *relative to* the major carbon-12 peak for each metabolite. I can see a couple ways to...do this: 1. Create a peaks-by-samples matrix populated by peak ratios rather than peak abundances, such that each cell contains the ratio between the 13C peak and the …

Metabolomics limma

updated 20 months ago • c53aba27

reads falling in each of my called peaks. However, each read represents a DNA fragment of a specific length, which can be estimated by cross-strand correlation analysis or known a priori. In my case, it is the length of one nucleosome...treat each read as being 147 bp long for the purpose of computing overlaps, since the number of bp sequenced is not representative of the fragment length. Would i…

updated 10.1 years ago • Ryan C. Thompson

I tried to get reverse complement of a DNA sequence in R applying Biostrings package. The length of sequence is around 900 and I want to see it completely but R shows an...TGCTTATCCATCTGACGCTTCAACAG   I would like to get the part in front of "seq" as a DNA sequence, completely and not with dots

biostrings subsetting View dnastring dnaseq

updated 10.4 years ago • arado1

reads from a BAM file, optionally trim the alignments, and then access the (possibly trimmed) query sequences. The first two operations--reading from the BAM file and trimming the alignments--can be accomplished easily with...GAlignments. However, my understanding is that query sequences are discarded when the GAlignments are populated from the BAM file. My first question is whether you have con…

[galignments] bam

updated 10.2 years ago • Robert K. Bradley

But 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 2.8 years ago • GenoMexa

on-line docu,mentation. I wonder whether the illustarted techniques (functions) for Pairwise Sequence Alignments are being usd in any of the packages aimed at predicting miRNA target-genes match. I only haveonly used...makes us of the Smith-Waterman algorithm. However I cannot recognize any of Biostring techniques for sequence alignment. I may be confused by the lack of documentation & co…

Alignment Alignment

updated 16.4 years ago • mauede@alice.it

Hi, I am trying to use Rsubread on the wheat genome ~17 Gbases. I have 32 GB of memory, most is available I am running R version 3.6.1 (64 bit), Rsubread version 2.0.1 I figured that the indexSplit command would...indexSplit = TRUE) Error 1: Check the integrity of provided reference sequences ... || || No format issues were found …

Rsubread

updated 5.8 years ago • bryan.penning

off-topic but I was wondering if anyone here knows where I might obtain a complete DNA or protein sequence for both BRCA1 and BRCA2? I retrieved protein sequence data from NCBI but I need to obtain two copies of each gene, i.e...one normal and another damaged for comparison purposes. I am unsure as to whether the protein sequences I have obtained are "healthy" copies. Thanks, ~Caitlin …

updated 13.1 years ago • Caitlin

<div class="preformatted"> Hello, Short summary version: How to interpolate a micro-array time series to get differentially expressed genes at a time point that was not measured? Long version: I'm analyzing a two species (human and mouse) and two groups (control and...Short summary version: How to interpolate a micro-array time series to get differentially expressed genes at a time point t…

limma limma

updated 11.8 years ago • Guest User

metadata you have available to extract. The h5ad files are composed of a cell by feature, such as **genes expression** and **peaks** & other **metadata**. So, a way to extract **expression data** or other related, is as described below...hdf5 file ```r sc_hippo <- Read10X_h5("/folder/file_name_hdf5_file.h5"). #set your file name ``` In this MTX each row represents a pe…

rna-seq Read10X_h5 atac modalities

updated 2.8 years ago • Cynthia

New to BioC, just trying to learn. I’ve got a sequence file (FASTA) and an annotation file (BED) with the various ranges of genes and other features. I would like to use the BED...file to annotate my sequence, and then be able to pull out portions of the sequence not found in the BE file (eg, 200 bp next to one of the genes listed

annotate

updated 7.3 years ago • Teeps

I have a set of genes with associated data that I want to locate on the mouse genome My approach is to * extract the genes in the genome * subset...the genes to include only my list * add the extra data for my list into the GRanges as metadata * export the relevant parts of the GRanges...object. <pre> MouseGenesGR <- genes(Mus.musculus, columns="SYMBOL")  head…

GRange

updated 9.4 years ago • mdeea123

actually working and I'm wondering if it is fine to start with reads mapped to genes instead of transcripts? Also, I'm looking for feedback on my data processing (especially exon lengths method) since I am...unable to find a straightforward tutorial for calculating gene expression from RNA-Seq data as most go to DEG analysis. Thanks for your input! PS if there is any issue, if you can advise re…

GeneExpression GenomicFeatures RNA-Seq TPM

updated 2.3 years ago • gingergeiger22

Hello, I am trying to analyze a barcode sequencing dataset. The experimental technique that generates the data is described here: [Chemical genomic profiling...a pool of gene knock-out mutants of a yeast or bacterium growing all together. Each mutant has a gene knocked out and is labelled by a unique...barcode sequence. We are counting those barcodes in each sample. The goal is to determine whic…

limma normalization sequencing edger

updated 9.6 years ago • Yury Bukhman

I want to change two things in this cnetplot 1. Exclude pathways in the graph 2. Providing gene names instead of the IDs   __1. __Using the example: <pre> require(dplyr) head(kegg@result) %>% select(Description, setSize...34 hsa04151 PI3K-Akt signaling pathway 320</pre> Let's say I do not want the genes for the `` Focal adhesion ``in the cnet gr…

clusterprofiler pathway analysis pathways

updated 7.6 years ago • Mr.RB

I am interested to get the chip name of the annotation databases for example hgu133a.db.``  I get the following information when I enter the database...name into the RStudio console. `` <pre> > hgu133a.db ChipDb object: | DBSCHEMAVERSION: 2.1 | Db type: ChipDb | Supporting package: AnnotationDbi...support/technical/byproduct.affx?product=hgu133 | EGSOURCEDATE: 2015-Se…

bioconductor annotationdata hgu133a

updated 7.8 years ago • Agaz Hussain Wani

a list of regions as my regions are 502 bp long sometimes they overlap with more than 2 distinct genes , for example `chr2:112541661_112542162` overlaps with both POLR1B and LOC105373562 ( the first gene is on + strand and the...seqnames , start=start , end=end) annotation<- annotatePeak(G.coor , TxDb = txdb ,level = "gene" , addFlankGeneInfo=TRUE ) and this message appears …

txdb R annotatation

updated 4.5 years ago • pegah.taklifi

DESeq2 to do differential expression analysis in a rather unusual system. I would like to compare gene expression between two closely related species (same genus). I have reference genomes for both. The RNA is just from control...species RNA-seq is to analyze only conserved exons, but because these species are so closely related--most genes in species A have a 1:1 ortholog in species B--that I'm …

deseq2 rnaseq across species

updated 8.5 years ago • vtartaglio

preferably Bioconductor that will compute the theoretical isotope spectra given the amino acid sequence. For example AYARATAYT should return these details. Most likely isotope combination: 12C44 1H66 14N12 16O14 Exact...0.008026484 etc another example where the major isotope is [M+1]/Z AYARATAYTRYTNNPPY Most likely isotope combination: 12C89 13C1 1H129 14N25 16O27 E…

Metabolomics proteomics MassSpectrometry

updated 5.1 years ago • Oliver

discovered some odd behavior with topGO. Given a set of the same (but differently ordered) list of uniprot id's, we are getting different enrichment results. I wasn't sure whether the ordering mattered. Or does the ordering...in non-microarray studies, btw, so we've faked the p-values (eg, 0.001) for the set of interesting genes. Thanks, Paul [[alternative HTML version deleted]] </d…

GO topGO GO topGO

updated 15.0 years ago • Paul Rigor

gt; Note: there are two suggested ways of importing estimates for use with > differential gene expression (DGE) methods. The first method, which we > show below for edgeR and for DESeq2, is to use the gene-level > estimated...counts from the quantification tools, and additionally to > use the transcript-level abundance estimates to calculate a gene-level > …

deseq2 tximport

updated 5.5 years ago • igor

div class="preformatted">Hello everyone, I wish to filter a list of Gene Ontology terms for the tip terms (most informative GO level) i.e. removing all GO terms which have more general ancestors

GO graph GO graph

updated 15.3 years ago • Aaron Weimann

the Illumina HumanMethylation27 BeadChip technology.  Here is an example of what some of the gene IDs look like: "cg00027083" "cg00035347" "cg00446235" "cg00563845" "cg00955230" How do I convert these ID's into the standard...gene names/symbols in R? Thanks

gene names methylation illumina convertids

updated 7.7 years ago • arbet003

I work on RNA-seq data from Oryza sativa Japonica (TaxID: 39947) There is only one genome sequence for this rice, but there are mainly two gene models. One system is known as 'osa' in KEGG, and it was from MSU-RGAP (http://rice.uga.edu...like 'LOC_Os03g02939'), and NCBI and phytozome (DOE) use its gene model. Another system is known as 'dosa' in KEGG, and it was from RAP-DB (https://rapdb.…

pathview KEGG Oryza_sativa

updated 2.6 years ago • jylee43

query(hub, c("homo sapiens","ensdb")) yes ensdb <- hub[["AH113665"]] gns <- genes(ensdb)library(AnnotationHub) hub <- AnnotationHub() query(hub, c("homo sapiens","ensdb")) yes ensdb <- hub[["AH113665"]] gns <- genes...x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence LRG_432. Note that ranges located…

EnsDb.Hsapiens.v86

updated 2.1 years ago • Shahenda

of differentially methylated regions. I can have a list of chromosomal locations indicating genes but I don't know how I map this location into specific gene names. > head(pns) [1] "chr19:4205395-4220723" "chr16:73793547-73835933...60540822-60563218" [5] "chr16:14630202-14638324" "chr19:49197954-49200178" Because I also have gene expression dataset, I want to integrate dna methylation…

Lung charm genomes Lung charm genomes

updated 13.5 years ago • Yoo, Seungyeul

Dear Bioconductor Forum, I am converting ensembl gene ids to hgnc symbols, but I am getting this error message I can't make sense of. Here is my code: seqdata <- read.delim("featureCount_Dup.txt...4 Warning message: In G_list$ensembl_gene_id == seqdata$Geneid) : longer object length is not a multiple of shorter object length Why has it not worked? Why am I only getti…

biomaRt

updated 5.1 years ago • Linda

Hi, I am writing because I am using UniProt.ws package for proteome retrieval. I'm trying to do this by giving as input the taxon ID for a certain organism. So I get the IDs with keys() and then I use select() to retrieve the information I need from each ID. The problem is if I try downloading the human proteome, the select() part is really time consuming. As an example: ```r library(U…

UniProt.ws UniProt

updated 5.1 years ago • JavierM

Hi all, I'm studying Agilent Human Gene Expression one color microarray using Limma. It results significant probes with the topTable function...I didn't succed to do the conversion of my identifiers with "ids2indices" function? nor later the gene set testing? Please, find below my code, I'm new to Limma what am&…

limma agilent microarrays gene set testing annotation

updated 9.0 years ago • Bouzid.a

of my project - just trying to add enough context. I am attemping to look at differences of abundances in shotgun metagenome samples that came from dust, specifically looking at gene abundances across contigs instead...the non-normalized reads from each metagenome back to the assembled contigs to get an idea of the abundances of these genes across the metagenomes (a community-function based ap…

DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion

updated 2.0 years ago • Linton

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...in excel and import the file back …

updated 22.5 years ago • Haddad, Ramsi

class="preformatted">Dear List, could anybody help on how to insert columns in TopTable for entrez gene id, gene name and symbol when using the hugene1.0ST arrays. When using the regular 3'IVT arrays such as the hgu133plus2...I used the following lines without a problem > *ebayes$genes$Symbol=getSYMBOL(ebayes$genes$ID, "hgu133plus2")* > *ebayes$genes$EG <- getEG(ebayes…

hgu133plus2 hgu133plus2

updated 15.1 years ago • Marcos Pinho

a compound binds to a target. I have drugs' SMILES and CHEMBL IDs. I have the protein's (targets) sequences and UNIPROT IDs. For drugs \[100 drugs\]: I converted drug SMILES to SDFset, and then I computed the fingerprints for each...Drug 2, 3, 4, ... 10. Then Drug 2 with Drug 1, 3, 4... 100 and so on until Drug 99 with Drug 100. I named this BASE\_DRUG\_KERNELS For proteins: I had the protein…

regression kernel ridge r

updated 9.3 years ago • ረ

<div class="preformatted">Bioconductors! New course material from Intermediate R / Bioconductor for High- Throughput Sequence Analysis is available at http://bioconductor.org/help/course-materials/2013/SeattleFeb2013/ There is a nearly 100...Bioconductors! New course material from Intermediate R / Bioconductor for High- Throughput Sequence Analysis is available at http://biocondu…

Annotation Visualization Cancer Annotation Visualization Cancer

updated 12.9 years ago • Martin Morgan

div class="preformatted">Dear all, How to filter genes from the expreSet by using the probe set names (affy)? Anyone has any clue on it? Thank you! Xin LIU</div

probe probe

updated 21.4 years ago • Liu, Xin

Hello, I wonder if anyone has come across the same problem as I am having. I am trying to map a gene name i.e HGNC symbol to its corresponding affymetrix probe using R/Bioconductor but I don't seem to be able to do it using

probe biomaRt probe biomaRt

updated 17.1 years ago • Ruppert Valentino

gene/DATA/GENE_INFO/Archaea_Bacteria/Bacte ria.gene_info.gz Column 2-6 should be (Entrez) GeneID, Symbol, LocusTag, Synonyms...expression changes with Pathview. But I have a problem. We got Locus_tags like BSU00010 and no gene IDs and I don't know whether Pathview can use it or not. I really don't understand the part about it in the vignette. So I thought...of converting them to UniP…

Microarray Annotation GO Bacillus subtilis gage pathview Microarray Annotation GO gage

updated 12.0 years ago • Luo Weijun

by the DESeq2 package: * I understand that the normalization is working under the assumption that most of the genes are not DE and only a small subset of genes are. I understand that this assumption is realistic in most experiments...when performing analysis across different human tissues. Meaning, does it make sense to assume that most of the genes will have the same expression levels in diff…

deseq2 deseq

updated 11.1 years ago • solgakar@bi.technion.ac.il

div class="preformatted">Hello, My name is Kevin Lee, and I am a PhD candidate in Bioinformatics at Georgia Institute of Technology. I have been trying to decide...CuffDiff2), I see the benefits of each. CuffDiff2 has the advantage that it quantifies isoform abundance, but it uses FPKM to "normalize" expression levels across samples. DESeq, however, estimates library size much more...be lo…

Normalization DESeq DEXSeq Normalization DESeq DEXSeq

updated 12.7 years ago • Kevin Lee

organism so I pulled annotation information from NCBI's gtf file, which has the symbols in a column named "gene". This turns out to cause some internal problem in `glimmaMA()` that tries to put the rownames into a column named "gene...efit <- eBayes(vfit) #This works: glimmaMA(efit, dge = dge) #Change SYMBOL column name to "gene" names(dge$genes)[2] <- "gene" names(efit$g…

Glimma

updated 4.6 years ago • Jenny Drnevich

annotation of probesets in affy GeneChips. I find that some times 2 probe sets refer to the same gene. For example, in the HG_U95Av2, there are 2 probesets (1369_s_at and 35372_r_at) both point to the same gene IL8. I wonder what...2 probesets would be affected by dye-labeling effect and hybridization effect in addition to mRNA abundance. What is then the point of having 2 probe sets which might…

Annotation probe Annotation probe

updated 19.7 years ago • Saroj Mohapatra

a variable that can be passed to justRMA (see ?justRMA for the help file). If you want the column names to be the cel file names, just do Data1 <- justRMA ( phenoData=pD1) exprs2excel(Data1,"spreadsheetname.xls") You will have...to hand enter 'Gene Names' in the first cell of the spreadsheet. You could probably hack the code for read.table() to get it to put 'Gene Names' in...all the CEL…

Microarray Genetics Cancer Microarray Genetics Cancer

updated 21.8 years ago • James W. MacDonald

I have a sample dataset derived from single cell RNA Sequencing with 1800 samples. Some genes have only few counts. Using WGCNA I can compute modules and even define the module...membership for each gene for each module. I want to find the number of counts for which a gene would be safely clustered into one (or 2) module(s). Would...it be valid to: Define genes with counts e.g. lower 5, by compu…

wgcna

updated 8.5 years ago • ly.leifels

salmon", txOut = TRUE) this yields txi, a large list of 4 elements, where: > attributes(txi) $names [1] "abundance" "counts" "length" "countsFromAbundance" I want to remove/exclude columns where there are >=4 0s in "counts." Counts

tximport Salmon

updated 4.2 years ago • Sheean