Bioconductor Forum

differ dramatically. In one of the pair wise comparisons, we have ~4200 differentially expressed genes (with fold change above 2 or below -2, p-adj<0.05), out of ~19,000 detected genes (human genome). DESeq normalization is based...on the assumption that most genes are not differentially expressed. Do you think that it is valid to use this normalization in this case? Thank you

deseq2 normalization

updated 10.2 years ago • GFM

how do I compare 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...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 the baseline. Howeve…

limma

updated 18 months ago • AL

Help with finding R tutors for microarray analysis, next generation sequencing and constructing gene interaction networks needed Hi I am a visually impaired bioinformatics graduate student...to best use the R packages for bioinformatics, especially for microarray analysis, next generation sequencing and constructing gene and pathway interaction networks.  This is very difficult for me …

bioconductor microarray network tutoring differential gene expression Job

updated 11.1 years ago • Thomas.F.Hahn2

I’m working with untargeted metabolomics data from samples that we run on two different column types (C18 and HILIC), both in positive and negative mode, for a total of four tables of (m/z + retention time vs. samples), which I generated using XCMS online. My goal now is to identify differentially abundant peaks, as one does with gene expression for RNA. I filtered features for a given table …

limma Metabolomics DifferentialExpression POMA

updated 3.0 years ago • wiscoyogi

GTL=eapply(GOTERM,function(x) { grep(term,x at Term,value=TRUE) }) Glen=sapply(GTL,length) names(GTL[Glen>0]) } ##usage GO.trans=GOTerm2Tag("transcription") ################ #Get GOID for all genes on ATH1 array ############# ##AffID.ATH1 is all...z$GOID) }) ############ #Find all genes that contain GOID whose GO term contians "transcrption" ############### ##function: Se…

GO affy Category GO affy Category

updated 20.2 years ago • Fangxin Hong

6\] Pf3D7\_01\_v3 \[251, 550\]      \*   -------   seqinfo: 14 sequences from an unspecified genome > data$totals \[1\] 1593882 2422822 1685087 3548254 > require(edgeR) > abundances &lt...aveLogCPM(asDGEList(data)) > summary(abundances)    Min. 1st Qu.  Median  …

csaw

updated 8.3 years ago • tangj

rely on alpha diversity similarities and based on the distances, classify ? NOTE: I only have the abundance matrices for both the genera and the phylum. I do not have the sequences

phyloseq

updated 3.7 years ago • Edmond

<div class="preformatted">Dear Colleague, We cordially invite you to submit a paper or invited session proposal to the upcoming 6th International Conference on Natural Computation (ICNC'10) and the 7th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD'10), to be jointly held from 10-12 August 2010, in Yantai, China. Yantai was listed as one of the world's most inhabi…

updated 16.2 years ago • ICNC'10-FSKD'10

attributes "description" from the ensembl database for Drosophila, it returned NA for all the genes. dmGeneList <- c("FBgn0000003 ", "FBgn0000008", "FBgn0000014") ensembl = useMart("ensembl",dataset="dmelanogaster_gene_ensembl...3 NA abd-A FBgn0000014 I searched the attributes with the name "description", searchAttributes(ensembl, pattern…

biomaRt getBM

updated 5.5 years ago • georgewwp

bit of navel gazing. I *think* I want to calculate alignment scores for subsets of already aligned sequences and I don't think there's an easy and efficient way to do this without having to realign the subsets of the strings...calculate the alignment score of the first half vs. the second half, or (say) running windows of length N along the alignment. Like I said, I *think* this is what I want…

Alignment Cancer Biostrings Alignment Cancer Biostrings

updated 13.8 years ago • Steve Lianoglou

package with some modifications. For example I did not normalized the data based on the number of sequences per gene, which would be the case for RNA-seq data. That is how my data looks like: ID C_WT C_WT C_WT PEG_WT PEG_WT PEG_WT...what I have is a table containing the proteins distributed per treatment…

Proteomics DESeq Proteomics DESeq

updated 13.3 years ago • Maia de Oliveira, Julio

I am running CEMiTool with an RNAseq dataset. I am using CEMiTool v 1.18.1 with R 4.1.2. I have an abundance table with transcript quantities aligned with uniprot accession ids derived from the starting RefSeq mRNA identifiers...with bioDBnet. I removed duplicates from the table and set the uniprot ids as rownames. The cemitool command below generated two modules although only one shows on the G…

GeneRegulation

updated 3.3 years ago • j.a.craft

Hi all The new Ensembl marts for release 87 are now live on [www.ensembl.org](http://www.ensembl.org/index.html). If you are using biomaRt, you can change your host to access our most recent data: ensembl\_mart\_87 <- useEnsembl(biomart=“ensembl") Change affecting all marts: Species dropdown now displays...www.ensembl.org/index.html). If you are using biomaRt, you ca…

ensembl ensemble mart ensembl mart biomart News

updated 9.1 years ago • amonida

span>_<span style="background-color:Yellow">Error in XXXX (peakAnnoList) :input object should be a named list (see example below).</span> _However, it all works for test files (provided with ChIPseeker) (see example below) Any advice...gt; plotAnnoBar(peakAnnoList) Error in plotAnnoBar(peakAnnoList) : input object should be a named list... > plotDistToTSS(peakAnn…

ChIPseeker named list error plotAnnoBar plotDistToTSS vennplot

updated 7.8 years ago • k.panov

I am trying to get the sequence of 200bp upstream of all zebrafish transcripts. I am using the following code: library(GenomicFeatures) library...31763] - [CGTTACTCTA...AGACACCACA] | 16586 NM_001256832 ------- seqinfo: 1061 sequences (1 circular) from danRer10 genome Now, I'd like to get those sequences in a character vector. I thought I could do: sequenc…

sequence bsgenome

updated 8.5 years ago • nicola.romano

I am very inexperienced with mathematics and expression data. I have developed a pipeline for WGCNA, practicing with gene-expression microarray data. I am now determined to try to apply this strategy to microbial-communities count data.  Initially I tried finding an adjacency matrix with the natural count-data: adjacency(df) And this indeed produced a set of plots- however…

limma voom voom counts

updated 9.5 years ago • chrisclarkson100

tximport to make a matrix of all TPM values, I have TSV files for many samples, which looks like: Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM ENSG00000187961.13 KLHL17 chr1 + 960587 965715 4,714223 2,219789...samples)) [1] TRUE > tmp <- read_tsv(samples[1]) Parsed with column specification: cols( `Gene ID` = col_character(), `Gene Name` = col_charac…

tximport

updated 6.4 years ago • HKS

is parasite genome). Our qPCR shows depletion of protein expression. However when we do RNASeq, the gene is not deferentially expressed. When viewed in IGV, we see high coverage in the UTRs and adjacent exons both at 5 prime...3 prime. When we remove UTRs from all the genes in the GFF file, the gene becomes differential (down regulated as expected). Is this a valid approach? We couldn't find any.…

edgeR DESeq2

updated 10 months ago • rohitsatyam102

div class="preformatted">Last week I extracted the 3UTR sequences for a list of genes identified through their Entrez_num. The biologist we are working with is not happy yet ... and asked...me to provide the following: Regarding the 3'UTR database I need for now the following: 1) UTR sequence 2) name of the gene 3) where the 3'UTR is located in the gene sequence. In other terms the coordina…

updated 15.7 years ago • mauede@alice.it

idx) # print(region) # print(sequence_only[, region]) # print(sequence_only) if (length(sequence_only[, region]) == 0){ len_ensembl <- length(ensembl_list) len <- length(sequence_list) ensembl_list[[len+1]] <- ensembl_id...sequence_list[[len+1]] <- "Sequence unavailable"; next } sequence <- seq…

ensembldb getSequence

updated 17 months ago • Melanie

few questions and read threads I think I have the right design and statistical test for looking for genes that change over time, however, I would just like confirmation if anybody can clarify, what the results output mean as...look for changes across time in general. I don't want an interaction term as I am only interested in genes that change across time, and thats it. I will do gene patterns la…

DESeq2 LRT multiple time points

updated 7.9 years ago • A

GSE24523. This experiment used a Nimblegen Microarray, platform GPL11164 and NimbleGen design name: 080501\_GDR\_Malus\_EST-V4\_EXPNimbleGen design ID: 7552.  Using the oligo and pdInfoBuilder packages I created...storageMode: lockedEnvironment) assayData: 193586 features, 24 samples   element names: exprs protocolData   rowNames: GSM618107\_144180…

nimblegen Biomart Uniprot

updated 9.1 years ago • theobroma22

using kallisto as our aligner. We are concerned that kallisto might struggle with high repeat sequences, and we've tried decreasing the number of kmers from the default of 31 to 21 and 25. Does anyone have experience with...using kallisto or other pseudo-aligners on high repeat sequences? or what might be the best aligner for high repeat sequences

Kallisto RNASeq pseudoaligners ShortTandemRepeats

updated 4.5 years ago • Shu Yi

of my own choosing/design. I am very interested in looking at the BRCA1, BRCA2, and Errb2/neu genes for evolutionary similarity and I would like to create a heatmap. Would this be possible? Would the data be available...from NCBI or GenBank? Wouldn't the sequence data on these databases be "general" (an aggregate)? Any suggestions on how I could proceed would be most appreciated

updated 13.2 years ago • Caitlin

I have several questions about analyzing miRNA sequencing data using limma voom. Most of these questions relate to the fact that the composition/distribution of miRNA sequencing...data is very different from mRNA sequencing data. 1) In comparison to mRNA sequencing where thousands of transcripts are often similarly expressed across...How about if I am interested in how a particular treatment aff…

limma voom

updated 9.9 years ago • Jake

Hi All, I have been using using DESeq2 to find differentially expressed genes between healthy and diseased groups but I do not have house keeping genes in the data set. Is it still possible to do DESeq...calculations without house keeping genes? and I do not have all the genes expressed across all subjects/samples (about ~4,000 genes in the data, at least 1 gene has a...sample with zero counts).…

deseq2 R

updated 8.1 years ago • gajender.aleti

<div class="preformatted"> I'm trying to use edgeR to analyse RNA-seq data following the guidance of "edgeR: differential expression analysis of digital gene expression data". I have done exactly as the manual told and when tapping the command "d <- DGEList(counts=d, group=group)", then...analyse RNA-seq data following the guidance of "edgeR: differential expression analysis of digit…

edgeR edgeR

updated 13.8 years ago • Guest User

104 | 56 | orf2 21 | 3 | My goal here is to descriptively show how gene expression for certain genes of interest changes across the samples, by describing fold-changes or by plotting normalised...but also gene length. In a single species, the length of a particular gene is the same in every sample; but for a microbial community of...this analysis: 1. Should the…

normalization edgeR metatranscriptome

updated 5.9 years ago • rachael.lappan

I would like to include gene symbols on a MA plot in the same manner as is implemented in the volcano plot command. I have been using the `` plotMA...I would like to include gene symbols on a MA plot in the same manner as is implemented in the volcano plot command. I have been using the `` plotMA ``command...plot commands: `` volcanoplot(data.fit.eb, coef = "IVIgiTreg_vs_n_iTr…

limma plot.MA volcanoplot oligo

updated 10.5 years ago • Gabriel Nathan Kaufman, Mr

Hi, I have developed a signed hybrid gene co-expression network using WGCNA and constructed module based on TOM followed by hierarchical clustering. I selected...a module which gave a positive correlation of the eigen gene module with immune score. When I look at the hub genes based on module membership >0.8, most of these have negative correlations...range (-0.23-0.028). Would somebody …

hub correlation eigen WGCNA

updated 4.1 years ago • mairah.khan

<div class="preformatted">Hi, (sorry for cross posting!) I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA...div class="preformatted">Hi, (sorry for cross posting!) I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Ada…

updated 15.4 years ago • blue jay

Currently, pathview does not take EC number as in put. But you may convert EC to KEGG or Entrez Gene ID using KEGGREST package. Then use mol.sum in pathview packge to map the EC based data to Gene ID based data. For example...library(KEGGREST) hsa.ec <- keggLink("enzyme", "hsa") head(hsa.ec) ? pathview::mol.sum HTH, Weijun -------------------------------------------- On Wed, 9/25/13, Ale…

KEGGREST pathview KEGGREST pathview

updated 12.3 years ago • Luo Weijun

I am currently working with Clariom D Human Microarray. After normalization of the data with RMA{oligo}, I get  138745   features which I need to annotate for the downstream analysis that includes differential expression and gene enrichment steps. I would like to assign a gene identifier to a given probeid using the select() function of {AnnotationDbi}: __>all.e…

annotation clariomdhumantranscriptcluster.db oligo

updated 8.9 years ago • yahia.adnani

Apologies for cross-posting on biostars, but the part most relevant to me involves procedures using Bioconductor packages. I'm working on a haplotype-resolved diploid assembly...Apologies for cross-posting on biostars, but the part most relevant to me involves procedures using Bioconductor packages. I'm working on a haplotype-resolved diploid assembly of a plant genome, where each chromosome is…

edgeR DESeq2 haplotype limma

updated 7 months ago • Paulito

really) -- if > gene/transcript length is not associated with the mean/variance > relationship for read counts, why was it asserted in the...RNA is fragmented, there will be a relationship between read counts (number of reads mapped to a gene model) and gene length. This is indisputable. The question is whether this is something we want to include in our model, beyond...Same with…

Normalization graph limma convert edgeR DESeq Rsubread Normalization graph limma convert

updated 13.6 years ago • Kasper Daniel Hansen

div class="preformatted">Hi all, I have a dataset consisting of sequence data from specific viral genes that I'm trying to correlate to data from indicators of disease outcome (CD4+ count

updated 18.1 years ago • Ian Cheeseman

SampleID) [1] FALSE Warning message: In colnames(HitCount) == myCondition$SampleID : longer object length is not a multiple of shorter object length ``` I then searched online and arranged my code as follow: ``` myCondition <- read_excel...in 'row.names' ``` This does not stop R to in the calculation but I get in my results that the row names are changed in numbers. Do you know how I…

DESeq2

updated 21 months ago • ussarizona

analyzed and pre-processed with limma. My first question is if i could similarly test for multiple gene sets regarding Gene Ontology via mroast. My design matrix for my expressionset is also mentioned in other post(https...length for each gene set for testing: __go2probe <- as.list(illuminaHumanv4GO2PROBE) govector <- unlist(go2probe) golengths...lt;- sapply(go2probe, length)…

limma mroast GSEA GO illumina human ht-12 v4

updated 10.6 years ago • svlachavas

Hi all, I am trying to determine the most appropriate design matrix to use for an RNA-seq experiment detailed below. Since my statistics knowledge isn't strong...Hi all, I am trying to determine the most appropriate design matrix to use for an RNA-seq experiment detailed below. Since my statistics knowledge isn't strong, I'd really appreciate some advice. ### Experimental design We have four…

DESeq2 limma modelmatrix edgeR designmatrix

updated 4.2 years ago • rebecca.lea.johnston

Greetings, I am wondering if someone knows a source of obtaining a list of the human tissue specific genes (ie. brain, liver,lung, etc.)? Is there a database of this sort to get the most recent list or any list? Thanks, Lana</div

BRAIN BRAIN

updated 21.5 years ago • Lana Schaffer

hi I want to analyze the TCGA data with the DESeq2 package. As you know there are three types of data in this database. This site (http://seqanswers.com/forums/showthread.php?t=42911) provides information on these three types of data. 1- raw counts: The (first) RSEM paper explains that the program calculates two values. One represent the (estimated) number of reads that aligned to a trans…

deseq2

updated 5.8 years ago • roohallah1435

in case I could generated them in an other way to get all the FDRs and fold changes for each gene. > class(Bgene) [1] "list" > names(Bgene) [1] "ttAll" "DownSameUp" > names(Bgene$ttAll) [1] "T11" "T3" "T19" "T19_T11" > names(Bgene$ttAll[1]) [1...T11" > names(Bgene$ttAll[[1]]) [1] "Row" "Column" "Block" "Name" "ID" [6] "…

limma ASSIGN limma ASSIGN

updated 19.3 years ago • daphne mouzaki RI

div class="preformatted">Hi, I would like to perform gene set analysis using global test or another method (suggestions?) but I only have 3 biological replicates for each condition...and I am not sure which method is the most powerful to use in this case. Also, has anyone compiled Biocarta pathways into gene lists for gene set analysis. regards

Pathways Pathways

updated 19.5 years ago • Anthony Bosco

and repeat the PCA the clustering in the PCA doesn't change much, neither does the heatmap of the most variable genes.. am I doing something wrong? Where/how will I see any effect of the RUV normalisation? What is the most appropriate...read_tsv 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 transcripts missing from tx2gene: 13365 summarizing abundance summarizing counts summarizing length > d…

deseq2 ruv batch

updated 6.3 years ago • r.tom

I want to deduct the coverage in one RleList from that of another. A - B. But the lengths of the coverages aren't going to be exactly the same, which means that the vectors will be rotated. This is not what I...For example, if the Rle in chr1 in A is longer than that in B I want to extend chr1 B with the length difference from A - B and value 0 to avoid rotation.   How do I do that?…

iranges s4vectors rle rlelist

updated 7.6 years ago • endrebak85

what is the simplest way to extract a table with the following information : -- gene\_name -- gene\_id -- transcript\_id many thanks ! bogdan &nbsp

gtf

updated 7.4 years ago • Bogdan

I am running DESeq2 to find associations between microbiome abundance and gene expression. The results include accession numbers that look valid but do not appear in the reference that...was used when calculating the gene counts and according to the ensembl ID converter were never valid ensembl IDs implying the problem is not that I used...the code that is running DEseq2 and consolidating the res…

deseq2

updated 6.1 years ago • JGibbons1

yet).  Because i want to compare rna-seq data from different sources, i want to remove the genes that are non-protein coding. This is due to wanting cleaner data ( some rna is rrna ).    So i downloaded the gene information...for homo-sapiens from the NCBI ftp server.  Now i have the deseq genes for example  assay(dds): <pre> …

r deseq2

updated 9.3 years ago • bioinformatics

Hi everyone, I am using the BSgenome package and annotations to retrieve several thousand sequences (22k) corresponding to a promoter microarray. Basically I run a loop through the whole list of chromosome name, start...and stop coordinates, and retrieve each 1Kb sequence using the 'subseq' function. When I run it, I get the following error *sometimes*: Error in get(name, envir = .classTable) …

Microarray Annotation BSgenome BSgenome Microarray Annotation BSgenome BSgenome

updated 15.6 years ago • J.delasHeras@ed.ac.uk

of using negative bionomial distribution to test whether a covariate is differentially expressed/abundant or not. I wonder, if the same argument is valid, when the analysis is not performing any test but for example, regressing...these genes over case/control. In this regression, one continue and use relative abundance or should still use say the variantestablizer

regression deseq2 counts

updated 10.3 years ago • akp

DESeq(dds, test="LRT", reduced = ~replicate + type + stage) ``` Looking on TPM counts of some genes, that interested me I noticed a problem. Genes, I assumed to be housekeeping, had decreasing TPM from first to last time...detected as differentially expressed. On RPF data these trend was not clear. Also I checked the genes with stable TPM, and they had significant adjusted p-value. …

DESeq2 timecourse time

updated 24 months ago • Anastasiia

div class="preformatted">Dear Group What the most convenient direct way of identifying sets of correlated genes ? Thanks a lot Alyaa -- Alyaa Mahmoud "Love all, trust a few, do

updated 13.1 years ago • Alyaa Mahmoud

keys=rnabindingterms, cols="GOID", keytype="TERM") once you got the GO IDs you can interrogate what genes have such a GO term annotated to them. currently this is not possible because the only key allowed is GOID: head(keys(GO.db...IPI" "PROSITE" "ACCNUM" [6] "ALIAS" "CHR" "CHRLOC" "CHRLOCEND" "ENZYME" [11] "MAP" "PATH" "PMID" "REFSEQ" …

GO AnnotationDbi GO AnnotationDbi

updated 12.7 years ago • Robert Castelo

code below). I was wondering if anyone has an idea about how to change the default affy-IDs as row names in a KEGG2heatmap (or GO2heatmap) to have gene symbols or gene names for that matter displayed in the heatmap. Changing...doesn't work either. I then tried to write the object of the function and recover the order of the genes from the rowInd, thinking I could change this post-plot in a way…

Annotation GO annotate affy Annotation GO annotate affy

updated 17.6 years ago • Celine Carret

<div class="preformatted">Vince S. Buffalo <vsbuffalo ...="" at=""> writes: > > Hi Bioconductor folks, > > I'm trying to create some GRanges summaries, but I think I may be missing > an obvious solution. I have fixed-width windows as a GRanges object, and > for each window/row I'd like to add a metadata column that indicates how > many…

updated 12.0 years ago • Charles Berry

seqname, ranges(gr), strand(gr), is_circular) 7: FUN(X[[i]], ...) 6: lapply(seq_len(length(grl)), function(i) { gr <- grl[[i]] if (length(gr) == 0L) return(DNAStringSet()) seqlevel <- grl_seqlevels[i] is_circular <- isCircular...idx <- match(seqlevel, x@user_seqnames) if (is.na(idx)) stop("invali…

R bsgenome getseq

updated 9.0 years ago • pm16057

alignments are excluded). I think from your original question you are really looking to provide the names of the sequences in your BSgenome object as a value to the chr.select argument of MEDIPS.createSet, I *think* chr.select...the BSgenome object. The initially reported error Calculating genomic coordinates...Error in vector(length = supersize_chr[length( chromosomes)], mode = "character") : …

Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer

updated 11.8 years ago • Vining, Kelly

3 options were proposed. 1. 50bp pair-end reads, sequencing each sample per lane --> we will get ~100 million reads per sample 2. 75bp pair-end reads, sequencing two samples per...lane --> we will get ~50-60 million reads per sample 3. 100bp pair-end reads, sequencing four samples per lane --> we will get ~30-40 million reads per sample Based on your experience, which op…

SNP Sequencing SNP Sequencing

updated 12.8 years ago • shirley zhang

Repitools is to characterize ChIP-seq coverage at different offsets relative to the position of the gene's TSS, but this gene has more than one TSS. I can think of a few possible ways to resolve this issue, all of which seem to have...1. Handle each isoform independently, generating a 3 separate promoter coverage profiles for this gene, based on the offset from each isoform's TSS. (The profiles…

repitools promoter tss annotation

updated 7.8 years ago • Ryan C. Thompson

use salmon, kallisto or any pckage that uses fastq files for that matter. To normalize, I need the length of the genes. This is my code to get the lengths of the genes: exons = exonsBy(EnsDb.Hsapiens.v86, by="gene") exons = reduce(exons...warnings like this: Warning messages: 1: In 10^9 * x/genelength : longer object length is not a multiple of shorter object len…

edgeR DESeq2

updated 3.4 years ago • JAcky