Bioconductor Forum

as 6 samples (max), and for two conditions there is one sample each.   Our goal is to select genes which are specifically expressed in some of these classes, so that the expression profiles of selected genes are similar...process (in DESeq2) we created a sampletable where we set as TREATED the samples for which the genes had to be 'specifically expressed' and the rest as 'CONTROL'. Of …

DESeq2 specific expression rnaseq clustering differential expression

updated 10.7 years ago • arrigonialberto86

that is essential. But, in that organism only three are known. If I have the expression for all genes, is it possible to cluster all expression in relation to expression of this three genes? I am looking if any of that genes...group together this three. I can do a cluster with all genes, but I would like to cluster one group knowing that another group exist. What you mean about my …

Organism limma Organism limma

updated 18.9 years ago • Marcelo Laia

hello everyone,   I came across a problem when I did GO analysis on differentially expressed genes derived from microarray using clusterProfiler . I gave a list of DEGs but failed to map any gene with the <span style...function.</span>   I used the following script to do the analysis:   “ data(geneList) gene <- names(geneList) gene hea…

clusterprofiler geneontology

updated 8.2 years ago • giuseppe0525

at mail.ndmctsgh.edu.tw> > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Get gene expression data by averaging probes > corresponding to the gene? > > I am trying to do a pooled microarray analyze with...data, > I have come to the idea to convert the probes in each array > to corresponding gene symbols, and use these gene e…

Microarray probe limma convert Microarray probe limma convert

updated 15.8 years ago • Gordon Smyth

a comparable data, I have come to the idea to convert the probes in each array to corresponding gene symbols, and use these gene expression data instead of probe expression as the data to analyze. I've tried to find a function...of averaging probes to corresponding genes, but found nothing that meet my need. I have done a few google searches like "bioc average probe intensity to gene", "biocond…

Microarray probe convert Microarray probe convert

updated 15.8 years ago • 697820169

Hello,  I want obtain groups of genes (for association genes with the phenotype), to be built from Gene Ontology. I used this script: <pre> > arraysdc.rma.gsc...AffyGenePDInfo"’</pre> <span style="line-height:1.6">The arrays that I used are </span>Human Gene 2.0 ST. Thank you very much for the help,  Santi

software error go microarray oligo hugene20st

updated 10.5 years ago • santi.cabellos

first time to analyze NGS data using R can any one clarify how to get GRanes() object with column Genes indicating which region (exons of experiment) belongs to which gene as in deepSNV example.. #========From deepSNV manual#========= Suppose...in folder ./bam and the regions of interest are stored in a GRanges() object with metadata column Gene , indicating which region (typically exons f…

deepSNV deepSNV

updated 11.5 years ago • Asma rabe

div class="preformatted">I noticed that the mas5 in affy command seems to include control genes (genes that begin with AFFX-) when scaling data. I believe Affymetrix excludes these genes. Perhaps this could account

affy affy

updated 22.6 years ago • osman@mit.edu

Enter the body of text here I just want to filter the protein-coding genes in redf.csv file. The gene list in redf.csv file is in geneID or symbol column. Code should be placed in three backticks...as shown below ``` # -- convert ENSG to gene symbol ens2sym <- AnnotationDbi::select(EnsDb.Hsapiens.v86, keys = keys(EnsDb.Hsapiens.v86), columns …

EnsDb.Hsapiens.v86 gene

updated 3.9 years ago • beslinail

I would like to convert hamster gene symbols to mouse gene symbols and tried hamster_genesymbol = annot_chinese_hamster$external_gene_name # gene list

biomart R ensembl

updated 4.8 years ago • rykerklie7

div class="preformatted">Dear expert, Is there some bioconductor package to update Gene symbol ? e.g. CRSP6 update to MED17. http://www.ncbi.nlm.nih.gov.ezp-prod1.hul.harvard.edu/gene/9440 KIAA0804 update...to VPS8 http://www.ncbi.nlm.nih.gov.ezp- prod1.hul.harvard.edu/gene/?term=KIAA0804 -- Best wishes, Jinyan HUANG </div

updated 12.9 years ago • Jinyan Huang

div class="preformatted">Hi there, Which packages and functions are commonly used for mapping mouse genes to homologous human genes ? Thanks, Zhihao [[alternative HTML version deleted]] </div

updated 15.2 years ago • Zhihao Ding

with the > way the HTSeq python scripts deal with the exons that overlap with more > than one gene ID. > > The solution that we had taken so far was that the gene IDs sharing an > exon were merged into an "aggregate gene...and our own experience, we know that it was not the most > appropriate solution: when the merged genes were differentially > ex…

DEXSeq DEXSeq

updated 11.9 years ago • Rao,Xiayu

Hello, I have performed a differential gene expression analysis on my bulk transcriptomic dataset which gave me 500-1100 significantly deregulated genes across...4 different comparisons. I have a list of about 75 genes of interest that may or may not be significantly deregulated across different comparisons. I want to make a summary

R subset DifferentialExpression

updated 3.3 years ago • Manav

are commonly used for RNA seq data if the goal is to identify monotonic increasing or decreasing gene expression over time or across stages using the results of differential gene expression analysis

DifferentialExpression rnaseqGene RNASeqData

updated 24 months ago • Shaimaa Gamal

I have 34727 genes in my gene universe. From those only 19622 have at least one GO term attached. Also there is  list of genes of interest...nbsp; Ontology:    -  BP  34727 available genes (all genes from the array):       - 467  significant genes.  1810 feasible genes (gen…

topgo

updated 10.4 years ago • s.apocarpum

Is anyone aware of a public resource (other than pubmed) for cataloging the influence of genes on one another? Ideally, a it would be a list of coefficients for the dependence of gene transcription on the products...of other genes and factors, such as d(gene(i))/dt=a(i,j)gene(j)+b(i,j,k)gene(j)gene(k)+...+otherfactors(i) . I'm fairly certain that we don't yet have this level...of knowledge, but…

updated 22.9 years ago • Jeff Sorenson

I would like to do a per gene ancestry covariate.  I believe this could be important because ancestry for portions of chromosome can be different...in the same individual so there is no way to correct across all genes with a simple covariate.   Is there any way to do this with DESeq2?  I am already using CQN to do gene length and GC

deseq2 ancestry

updated 9.0 years ago • kodream

if conceptually I can use the DESeq to test for differential transcript expression compared to genes. In our case we have generated a transcript model based on RNA-Seq and if we try to collapse those transcripts to genes...in order to do gene level differential expression many exons are collapsed to give rise to artificial exons. eg : Transcript 1 : ---------------------- (exon) Transcri…

DESeq DESeq

updated 14.0 years ago • Abhishek Pratap

Hi. I want to use the genefilter library to perform simple t-tests for each gene comparing across leukemia and normal samples. And I need the pvalues, so here is the code I have used to prepare the rowttest...LeukemiaType, "NoL") factor(cml_normal$LeukemiaType) ##This code maps the ENSEMBL IDs to gene symbols and ENTREZ IDs and adds them to the feature data library(org.Hs.eg.db) symbols = map…

rowttests

updated 4.0 years ago • leonardorosas2001

Hi, I would like to carry out a gene set enrichment analysis using gene sets designed by an expert (ie lists of carefully chosen genes). The tools are numerous

gene set analysis

updated 10.4 years ago • SamGG

not (within the background noise). This is similar to the MAS5 detection calls, but Exon 1.0 ST and Gene 1.0 ST Arrays don't have mismatch probes, therefore MAS5 cannot be used. According to Affymetrix, the DABG is not valid...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 d…

probe xps probe xps

updated 15.3 years ago • Pascal Gellert

I'm right now working with a RNA-seq raw count data file (in .txt format). It's a matrix of ~50,000 genes (row) and 8 samples (column). My assignment is to get differential gene expression analysis. But I'm not really sure what it...questions are: 1) What does one expect from differential expression analysis? I've got the list of genes that have p-values less than 0.05. Would that be sufficient…

deseq2 bioinformatics rna-seq Tutorial

updated 9.3 years ago • fromhj304

div class="preformatted">Hi All, Is there a way to identify the genes that contribute to the gene set enrichments calculated by roast/romer? I realize that all of the genes in a given set are...contributing to the p-value calculation, but is there a way to get at, for example, the genes that contribute to the "PropUp" value in the output of roast? And is the analogous gene set knowable in the…

updated 12.0 years ago • Stephen Hoang

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

Hi, after I added gene description to `` y <- DGEList(counts=rawCountTable, group=group, genes = merged.descriptions) `` the gene names have replaced...by numbers > logCPM <- cpm(y, prior.count=2, log=TRUE) > head(y$genes) gene_name gene_description 3 sp0000003 &am…

heatmap.2 edger

updated 8.3 years ago • mictadlo

br/> $ALPK3<br/> [1] "57538"</code> As far as I can tell, "MAK" is correctly mapped to the gene ID 4177 and incorrectly mapped to the gene id 57538 (the latter is the id corresponding to gene symbol "ALPK3"). Am I misunderstanding

org.hs.eg.db annotation error

updated 9.5 years ago • af2202

Hi, I am using edger to analyze RNA-seq data. I have generated count table for each genes under each condition. However, my goal is not to look at differential expression of specific genes. Instead, I want to look...at differential expression of some gene families. For example, I have gene A1, A2,...,An under gene family A . I want to see whether gene family A is differentially expressed...My que…

edger

updated 7.8 years ago • zhou_hye

Hi  I have level3 RSEM gene data with raw counts. I want to find the differentially expressed genes using edge R but the problem is raw counts seems

rnaseq edgeR

updated 8.3 years ago • lily

Hi, I am trying to figure out how to calculate the expression of a gene via GenomicFeatures and IRanges. My solution to this is based on the idea where I find group the TxDb by genes, then see if...how many transcripts are "above" the gene, that is how many are overlapping, within the range of the gene. This includes obtaining the RNA-seq data from UCSC, then...TxDb.Hsapiens.UCSC.…

genomicranges iranges

updated 10.8 years ago • cookie

testing problem of microarrays is for you to a priori identify a particular list of genes you're interested in, and then you only have to do the multiple test correction for this smaller list. I've never done...smaller list. Obviously, all the data preprocessing and normalization will be done with all the genes, but should I pull out the genes before f…

Normalization limma

updated 10.8 years ago • Jenny Drnevich

Dear Colleague, 1. I am using the WGCNA software to construct a gene co-expression network and identify several modules. The aim is to find out the top 100 hub genes for each module. I only find...a function called chooseTopHubInEachModule which is able to find one top hub gene for each module. In my case, do you have some advice on how to get the top 100 hub genes for each module in a stra…

WGCNA co-expression network RNA-Seq

updated 7.9 years ago • wangdp123

div class="preformatted">I have a list of 80 genes in a txt file and I am looking to use a data base, for example NCBI to get information on each of these gene. I need get the start...and the end base pair position for each gene listed in my file? Any idea how to get started or what to use? Your help is greatly appreciated [[alternative HTML version

updated 16.7 years ago • Kay Jaja

I am facing problems in setting up pathway enrichment analysis for the differentially expressed genes because of problems with Gene Ids. I tried using DAVID but the species that I am using is not listed there. In brief, I used...Info/Index/ for RNA seq data analysis. I have the list of up and down-regulated genes. I am trying to do gene enrichment pathway analysis for the up and down-regulated…

GeneIDConversion AnnotationForge

updated 4.8 years ago • AbhilashKumar.Tripathi

div class="preformatted">Dear Steve, The genes that contribute most to the roast result are the same genes that are ranked at the top in a standard genewise DE analysis...i.e., ranked by topTable(). Roast doesn't output the leading-edge genes because they are already available from the standard genewise analysis. The z-score is computed from the moderated...and z > sqrt(2). The prob…

updated 12.0 years ago • Gordon Smyth

Hello, I am trying to find GOs for a set of genes. So, not performing an enrichment, but only collecting the GOs where a certain gene is involved. Since I have a great amount...of genes to look for, I would like to either performing the search via a REST API or mapping it via a downloadable file. So far I have...found Ensemble sufficient for providing me GOs for single genes and species. But w…

GO ensembldb

updated 2.2 years ago • Rockbar

The codes and instructions for annotating gene names to the result table for differential gene expression analysis in DESeq2 seem to be for using Ensembl as the reference...genome in the alignment step. I'm wondering if there are instructions/codes for annotating gene names if I used UCSC hg19 as the reference genome in the alignment step? Thanks for your help

deseq2 gene names differential gene expression

updated 10.8 years ago • anpham

div class="preformatted">Dear all, Given a gene of interest, is there an easy way to get the n nearest genes either side (i.e. 5' and 3' direction) on the chromosome, without leaving...R? I looked in biomart for a way to get the nearest gene either side but couldn't see anything obvious. If this exists I suppose that could be one way, just repeat the getBM call

GO biomaRt GO biomaRt

updated 14.5 years ago • james perkins

I was told they quantification was performed like so: "We used subread to summarize counts to the gene level." These are the parameters that I am using: ``` mock1 <- featureCounts(files="mock1_Aligned.sortedByCoord.out.bam...and not gene? I have performed Differential expression with GTF.featureType set to both exon and gene and get differences in my top...DE genes. I would expect the r…

Subread RNASeq featureCounts quantification

updated 3.2 years ago • Sara

Hello, I ran camera() in edgeR to test whether 2 gene sets are highly ranked in my mutant data compared to my wild-type data in terms of differential expression relative...Hello, I ran camera() in edgeR to test whether 2 gene sets are highly ranked in my mutant data compared to my wild-type data in terms of differential expression relative to...other genes. design <- model.matrix(~0 + g…

gene set testing camera edger

updated 9.5 years ago • le2336

I've noticed that there are a lot of genes (>1/3 of total) which have names and/or symbols in NCBI that are not in the reference annotation files. The oviAri4.ncbiRefSeq.gtf...problem, I have used the following code: First I import the gtf file and find the total number of genes, and the total that have a LOC gene ID. ``` txdb <- makeTxDbFromGFF(file=gffFile, format=c("gtf")) txdf …

Annotation RNAseq

updated 4.7 years ago • Chris

div class="preformatted">Hello all, I have list of differentially expressed genes from an rna-seq analysis. Also, I have a two-column annotation file for the organism with the columns being gene and goterm...bioconductor package or any other tool that I could use my list and annotation file as input and do gene set enrichment analysis. Thanks, Al [[alternative HTML version deleted]…

Annotation Organism Annotation Organism

updated 13.1 years ago • Alpesh Querer

div class="preformatted">hi I am interested to find out the genes that are positively and negatively correlated genes with my genes of interest. (using rnaseq normalized expression

updated 11.4 years ago • Guest User

Hello, I've come across several gene set enrichment tools aimed at summarizing DE genes in RNA-seq datasets, but I have a slightly different goal, and I'm wondering...differences between species based on KO presence/absence. For instance, one lineage has many more genes associated with flagellar function, whereas another has a more complete photosynthetic apparatus. Maybe this question

gene set enrichment KEGG

updated 7.9 years ago • RMRG

Hi, I want to find if one gene has a significantly different Log2FC than a different gene. (e.g. Gene A has LFC of 2.5, and gene B has a LFC of 2.8 - are they significantly...One way I'd thought of is to use the LFC and standard error calculated by DeSeq2 for each gene and calculate T test using this. Unfortunately I'm not sure if this is a reasonable approach. Any pointers would be great

DESeq2

updated 2.7 years ago • Matt

preformatted">Hello all, I was just wondering if there is an easy way to start with a list of Gene Ontology terms and to end with an interpretable map of their inter-relationships. This would hopefully either connect...are siblings/parents/children of one another or would spit out an induced GO graph with the listed Gene Ontology terms labeled. The reason I was wondering if something li…

GO GO

updated 18.6 years ago • davidl@unr.nevada.edu

Hello ! I'm looking for a tool (R or API if possible) which for a given pathway return genes and/or metabolites involved in it and their function in the pathway. Thanks in advance for your help

gene metabolite functionnal annotation pathways

updated 5.8 years ago • emisecherre

div class="preformatted">Hello, I have a question regarding the gene model source to use with DESeq. Assuming the following workflow: 1. Map reads to genome (bowtie/tophat/bwa/etc). 2. Count hits...is about step 2: What is the recommended gene model to use when counting hits-per-gene ? RefSeq-Genes, UCSC Known Genes, Ensembl Genes and others come to mind, but those...usually contain multipl…

DESeq DESeq

updated 13.8 years ago • Assaf Gordon

I am trying to map Transcript ID's of the HuGene-1\_0-st-v1 affy chip to their corresponding Gene Symbols. When I do this I am often getting multiple gene symbols for Transcript ID's.  ex:  8029669 -->&nbsp...CT47B1 /// CT47A12 /// CT47A5 /// CT47A10" What would be the best way to choose one of the gene symbols? Also are there any biocondu…

transcript_id gene symbol

updated 10.4 years ago • Jo

Hi everyone, I'm new to RNAseq analysis and I have a general question about how to treat genes in DESeq2. Initially I estimated transcript counts in salmon and then imported (tximport) them into DESeq2. Transcripts...were converted to genes using the EnsDb.Hsapiens.v86 database, gene counts were estimated and normalized and those became the units (rows...of my DESeq2 analyses. But many of thos…

deseq2

updated 5.6 years ago • mlosada323

then mapped the affymatrix probe IDs to EnsEMBL ID by EnsMart. I am interested in whether some genes are present or absent (binary) in given samples. I have a question: if several different probes reprenting the same gene...have the different P/M/A calls, are there any strategies for determing whether the gene is present or absent in the sample? Wuming </div

Microarray probe Microarray probe

updated 20.6 years ago • Wuming Gong

I am looking to use customproDB with my bam files, vcf and gene fusion data to generate custom peptide sequences. I am particularly interested inbcr gene fusion events. I was going...through the documentation and was not quite sure how to represent my gene fusions in the bed file so that they will be picked up by the software based on the categories in the JunctionType labels

fusion bed files gene fusion bed file

updated 9.9 years ago • ramaniak

div class="preformatted">Hi, For an RNA-seq data, I have found the significant DE genes based on FDR < 0.05 using the exactTest() function. Now I need to rank these DE genes based on the expression level (count

updated 13.1 years ago • Fatemehsadat Seyednasrollah

I'm using GSVA (v1.18.0) on R 3.2.2 and trying to perform a gene set analysis on a small data set (75 genes, 6 samples). However, whenever I set the bootstrap rounds to > 10, I end up with a segfault...I'm using GSVA (v1.18.0) on R 3.2.2 and trying to perform a gene set analysis on a small data set (75 genes, 6 samples). However, whenever I set the bootstrap rounds to > 10, I end up…

gsva segfault

updated 9.7 years ago • Rajarshi Guha

Hi, Sorry in advance if the question is too "newbie " : I have 3 data sets : 1. 8000 genes 2. From this 8000 i have 200 that were found significant for a specific disease im analyzing . 3. Another data set with genes...associated with another disease . I want to preform gene enrichment analysis with this 3 data frames and as I understand a test that uses hyper geometric distribution…

analysis R GOfuncR

updated 2.6 years ago • Eliza

0 of individually 2906 all 2906" [7] "Missing genes on chr 7 0 of individually 2818 all 2818" [8] "Missing genes on chr 8 607 of individually 2385 all 2385" [9] "Missing genes on chr...9 1892 of individually 2303 all 2303" [10] "Missing genes on chr 10 0 of individually 2216 all 2216" [11] "Missing genes on chr 11 0 of individually 3190 all 3190" [12] "Missing genes on...chr 12 0 of individual…

biomaRt biomaRt

updated 12.0 years ago • Guest User

are missing their RNA ends and almost as many are missing either a 5' UTR or a 3' UTR. /nb/dario/genes$ egrep -c "(HAVANA|ENSEMBL) transcript" gencode.v17.annotation.gtf 194871 /nb/dario/genes$ egrep "(HAVANA|ENSEMBL) transcript...gencode.v17.annotation.gtf | grep -c mRNA_end_NF - 21699 /nb/dario/genes$ egrep "(HAVANA|ENSEMBL) transcript" gencode.v17.annotation.gtf | grep -c cd…

Transcription Annotation Transcription Annotation

updated 12.4 years ago • Dario Strbenac

with isoforms.results from RSEM analysis. I am trying to annotate my deseq results with symbol and entrez IDs, following the vignette http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst...lt;- c("row", "ensembl_gene_id") res <- merge(res, annot, all.x=TRUE) #Annotating symbol and entrez IDs with mapIds res$symbol <- mapIds(org.Mm.eg.db, …

DESeq2

updated 2.4 years ago • Maka

div class="preformatted">Hi All, I have a list of genes and I want the snps matching of these genes (the other way too e.g: Snps ----> genes) Is there any R package to do this ? Regards

updated 16.4 years ago • Mohamed Lajnef

<div class="preformatted">Hi, This question regards how various gene set testing methods deal with pre-filtered (non-specifically) data sets. Dont genes in a gene set that did not pass a filter constitute important evidence against that gene set? Not taking them into account when calculating whatever gene set summary statistic seems wrong (e.g. as recommended in chapters 13 & 1…

updated 14.6 years ago • François Lefebvre