Bioconductor Forum

Dear Dr. Smyth, We are analyzing some RNA-seq samples collected in different batches, where the batch is a known variable. To account for that we reasoned we could use a linear model to include the batch effect and then remove it.  Since the voom+limma approach is shown to work well for differential gene expression, we thought of estimating the weights for each observation through voom…

voom limma clustering removebatcheffect() batch effect

updated 10.5 years ago • ale.breschi

div class="preformatted">Hi All: I would like to display all the differentially expressed genes that I got for 4 different treatments (respect to the control) onto a heatmap plot, in such a way that they're ordered respect...to their expression values. My questions are: 1- Is there a way to make a heatmap for around 10000 genes (the "union" set from all differentially expressed genes) withou…

updated 15.9 years ago • avehna

use the annotation packages (e.g. library(hgu133a.db)) to get the assignment between probesets and genes. Are there any functions, methods (median, mean,...), literature how to combine probesets to genes? I want to run some network...analyses on gene level. Therefore I need some kind of 'gene intensity'. Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians

Microarray Annotation Normalization Preprocessing Network Microarray Annotation Network

updated 16.8 years ago • Markus Schmidberger

preformatted"> Hello, The following are the command lines that I have been using to filter out genes with small profile variance from gene expression data by Matlab. ---------------------------------------------------------------------- % filter genes with small profile variance % less than

updated 11.9 years ago • Jerry Cholo

I have a research problem that I want to solve. Basically, I want to find important genes per module that is generated from WGCNA algorithm. I define important genes as hub genes. Hub genes is defined as...genes that have most connectivity. I read from some paper that basically the calculation is to sum all the weight of each node...it from the highest to smallest, and select top 1%,5%,…

wgcna

updated 8.0 years ago • bharata1803

div class="preformatted">Dear Bioconudctor, I have this question about how to compress the gene expression dataset from probe sets denoted to gene denoted values. The analysis has two simultaneous goals, first is...to convert the probe sets to gene names. Second is to convert the probe sets values into just one summary gene expression value of the associated gene. For...gene? Another ques…

Annotation probe convert ASSIGN Annotation probe convert ASSIGN

updated 15.1 years ago • Xiaowei Guan

div class="preformatted">Hi, I am trying to run a HyerGTest with GOstats on a mouse genome entrez IDs. The Ids I have imported from biomart: entrez_data_1 <- getBM(attributes=c("mgi_id","entrezgene"), filters= "mgi_id", values...I Than tried to run the HyperGTest command with success MmOverBP <- hyperGTest(paramsBP) MmOverBP Gene to GO BP test for over-representation 3146 GO B…

Annotation GO GOstats Annotation GO GOstats

updated 14.8 years ago • Assa Yeroslaviz

I have performed a diffential expression analysis on RNAseq data of 17 treated and 21 untreated samples using **DESeq2_1.22.2**. The results look good except for a gene showing a log2FoldChange < -20. I found a strong discrepancy between the DESeq2 log2FoldChange (-24.72) and the one calculated manually (-2.24). Have I missed something or why is there such a big difference? &…

deseq2 RNAseq

updated 6.8 years ago • Matthias Munz

I have transcript abundance data (obtained with kallisto), which I converted into non-normalized gene-level counts with tximport. In my resulting count matrix, each gene has an Ensembl ID. Before running DESeq2, I converted...the gene Ensembl IDs into gene symbols. However, it so happens that a few different Ensembl IDs map to more than one gene symbol. Thus...in my count matrix, 16 genes are dup…

DESeq2 RNAseq

updated 5.4 years ago • Nikolay Ivanov

Hi, I am using DESeq2 for traditional RNAseq data analysis for finding genes that their expression level changed and I am also looking for genes that their level did not change. I later take these...two groups of genes are characterize each group. I wanted to ask you what is more correct for taking the unchanged genes: are these all the...genes that did not get a significant padj value or shoul…

deseq2 lessAbs

updated 7.7 years ago • raya.fai

Diseased samples, using edgeR. I take the entries with FDR < 0.05. Out of a total of around 57700 genes (including the multiple isoforms), I have obtained around 11500 genes within my selected FDR. However, among these, I find...data is biased towards a particular set. Furthermore, when looking at the log(fc), the upregulated genes have a max value of 7, while in case of downregulated ge…

edger differential expression genes fold change

updated 6.6 years ago • ilovesuperheroes1993

data using the mas5calls function in Affy package. For example, I would like to only look at genes which are called present at least twice in 20 chips, and remove genes which are always absent. Not sure how to go about this

GO affy GO affy

updated 22.1 years ago • Anthony Bosco

If I want to identify gene which express in one condition. Is it possible in deseq2. Because I think Deseq2 calculate logfoldchange for the gene...that express in two condition  and test statistic for significant gene. However it will produce the gene that express in higher or lower but not the gene that not express.   For Example, the...gene express in treat condition not in …

deseq2

updated 7.9 years ago • naktang1

Hi all, I use the “annotate” package to convert affymetrix 3’ probe to gene ids. For some probes it does not find corresponding gene ids. For example, searching for “1368587\_at” and “1385248\_a\_at” gives...getSYMBOL(c("1368587_at","1385248_a_at"),"rat2302")</pre> But when I google "1385248\_a\_at", I get gene symbol “Ogn” (gene id: 291015) in rat genome database. When I used biomaRt - …

annotate biomart probe to gene id

updated 11.2 years ago • rafi A

I am not able to retrieve my genes contributing to the GO term being enriched. Code should be placed in three backticks as shown below ```r #this is my code...I am not able to retrieve my genes contributing to the GO term being enriched. Code should be placed in three backticks as shown below ```r #this is my code allRes <- GenTable(hs_topGOdata, classicFisher = resultFi…

gene enrichment topGO GO retrieve

updated 2.8 years ago • Priya

gt; >For 3 experimental groups, how can someone extract >differentially expressed genes which is common in all >three groups? What you do mean by "common in all three groups"? Do you possibly mean, significant...for all three contrasts? That would imply looking for genes which have different expression values in all three groups, which is sort of the opposite of what you hav…

limma limma

updated 20.8 years ago • Gordon Smyth

Hello. I am trying to create a GeneRegionTrack using Gviz. I would like to display the gene symbol rather than the Ensembl transcript ID in the gene track. Please see below: ```r gene <- GeneRegionTrack(TxDb.Hsapiens.UCSC.hg19.knownGene...name ='Gene', showId = TRUE, transcriptAnnotation = "symbol", geneSymbol = TR…

Gviz

updated 3.6 years ago • hsf378

In the following example 'selectedEntrezIds' is a list of 1507 non- duplicated modulated ENTREZ ids, included in 'entrezUniverse', a list of 3122 non-duplicated ENTREZ ids taken as the universe. Here is the code: > hgCutoff

GO GO

updated 18.9 years ago • Ariel Chernomoretz

class="preformatted">Hi, everybody, I was wondering whether there is a package to cluster a list of genes to different GO categories my problem is as such: i have a list of genes (a tab delimited file): id flybasename_gene flybase_gene_id...1622894_at CG15120 FBgn0034454 37248 protein binding I would like to try and group the genes in various GO categories, which are menti…

Annotation GO Annotation GO

updated 15.0 years ago • Assa Yeroslaviz

div class="preformatted">Hello All, I am using DESeq for identify differentially expressed genes among a couple of samples. At the end of the calculations i write the results to 3 files as follow: resSig <- res[ res$padj...the DESeq paper it is mentioned that the last two lines of code extracts the up and downregulated genes, So I'm thinking the sum of the number of genes in (Do…

DESeq DESeq

updated 13.8 years ago • OD

to note that these sample can contain certain cancer related mRNAs. I just wanted to say which genes was 'expressed' in my samples, so I wonder if it is okay to say it is expressed when the read count is 1 or more and not if the...qPCR later if needed). To my understanding, for example, in micro-array, I cannot claim that a gene is expressed because there are background signal so the low pos…

RNASeqData RNASeq

updated 3.5 years ago • Pang

that I can't seem to find an answer to by searching the BioC lists. I want to use GOstats on a gene list. I've read the vignette and understand that defining the gene universe is an important step. The vignette outlines...various non-specific filtering steps that can be done on an expression set in order to define the gene universe. My question is are the non-specific filtering steps done on a no…

GOstats GOstats

updated 18.3 years ago • Rachael McBride

problem when using the KEGG annotation with hyperGTest: Somehow hyperGTest does not consider all genes. In the example below, all three genes are in the category "05020" (this is what mget(genes,envir=org.Hs.egPATH) says). In the...summary of hyperGTest, however, the category contains only two genes. Is there an explanation of this behavior? Thanks in advance! Anne > library("Category") …

Annotation Category Annotation Category

updated 15.8 years ago • Anne Kupczok

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...DOE) use its gene model. Another system is known as 'dosa' in KEGG, and it was from RAP-DB (https://rapdb.dna.affrc.go.jp/; like 'Os03g0121300...RAP-DB and E…

pathview KEGG Oryza_sativa

updated 2.6 years ago • jylee43

1.32.0) under two different approaches (as described below) and I’m getting different numbers of genes per GO category. __\#\#\# Approach 1 \#\#\#__ <pre> > library(goseq) > gene.vector = as.integer(assayed.genes%in%de.genes) #19,792 total...genes (502 DE genes) > pwf = nullp(gene.vector, "bosTau4", "ensGene") > GO.hiper = goseq(pwf, "bosTau4", "ensGene") …

goseq biomart

updated 7.6 years ago • frezende

strains with three replicates for each condition: ![enter image description here][1] and the gene ontology for the reference strain N402 is as follow: ![enter image description here][2] so how is it possible to combine both...files using R? or other method? second which package, should i use for the gene ontology analysis. is it possible to cluster the different genes using mFuzz? than…

gene RNAseq fold ontology change

updated 4.6 years ago • najib

hgdownload.cse.ucsc.edu/goldenPath",   miRBaseBuild=NA) \#Sort the exons of the Txdb by gene exons<-exonsBy(Txdb, by="gene") \#SummarizeOverlaps to count unique reads library(BiocParallel) se <- summarizeOverlaps...sig=subset(res, padj<=0.1) sig=subset(res, abs(log2FoldChange)>=2) \#Save sig and gene list as csv file write.csv(sig, "…

deseq2 results rstudio

updated 10.5 years ago • Lillyhchen

As you can see, in the first column is missing the header `Gene_ID`. I have tried to retrive the gene symbol using this code, but apparently VDAGs aren't either `"ENTREZ"` or `"ENSEMBL"` IDs. I did use `AnnotationDd` and made my own

EnhancedVolcano

updated 19 months ago • Patadù

I have a set of genes from an RNA-seq dataset generated from Wild type and mutant samples. As expected there are a number of genes that significantly...differ in gene expression as called by Cufflinks/cuffdiff. I am trying to create a scatterplot where the genes that significantly change...in expression are colored differently than the genes that do not (ex.: Up = red, down = blue, NS = bla…

cummerbund

updated 8.6 years ago • markus.nevil

model organism using the limma+voom pipeline. Next, I wish to look for functional enrichment of DE genes using GOseq. I successfully used GOseq on my data set by following the GOseq vignette, using custom gene lengths and GO...mappings. However, I note that following the vignette leads to **all** DE genes being tested for enrichment regardless of the direction of differential expression (i.e.…

goseq

updated 6.7 years ago • charles.foster

I notice that some mouse symbol will return multiple human gene symbol. Below is an example. If i search the mouse id on gene card, the correct human homolog should be ZNF286A, and Tmx2 is...hsapiens\_gene\_ensembl") mouse = useMart("ensembl", dataset = "mmusculus\_gene\_ensembl") genes = c("Zfp286", "Tmx2") genes = getLDS(attributes = c("mgi\_symbol"), filters = "mgi\_symbol", values = …

biomart gene symbol

updated 10.5 years ago • chang02_23

I have normalized my libraries for library size and composition, have filtered out lowly expressed genes (with a count of <10) and did a glmQLFTest. Using the decideTests function I get the following output: summary(decideTests...the glmTreat function where I use a FC cut-off of 1.5 (or logFC cut-off of 0.58), I only retain 19 genes! tr <- glmTreat(fit, contrast =…

EdgeR Bioinformatics Transcriptomics Quantseq

updated 4.4 years ago • Barista

I am trying to perform enrichment analysis with reactomePA (R package) on a smaller list of genes (477) and I have a problem with organizing the dataset. As far as I understood the input file should contain only two-column...Entrez ID (column n.1) and fold change (column n.2). I converted the ensemble ID with Biomart with the online tool, and then created...decreasing = TRUE) head(geneList) …

r reactomePA enrichment

updated 5.6 years ago • camillab.

div class="preformatted">Dear list, can anybody suggest how could I insert gene names in additional to gene symbols on my topTable generated by limma with my differentially expressed genes? cheers

limma limma

updated 16.3 years ago • Marcos Pinho

I am writing this mail for second time. I wanted perform a pca analysis ,for each cancer type and genes of interest expression. I just wanted to plot only a single point which is able represent each cancer and their genes...expression .Can you please explain me on it.( And cancer per gene basis should i take median or mean values to represent their expression). Thanks in advance. -- output of…

Cancer Cancer

updated 11.5 years ago • Guest User

In the moment, I am interested in how my conditions differ in terms of expression of a subset of 36 genes. The idea is to count only the reads, which correspond to those 36 genes and use this piece of data for the analysis of their...expression across the conditions. Will this approach be valid? What is the minimum number of genes required by the statistical model implemented in DESeq? I apologiz…

RNASeq RNASeq

updated 13.9 years ago • vladimir mashanov

I am trying to analyze the DE genes from rna-seq data, but when I try to use the goana function I get the error message "No annotated genes found in universe...I believe this is because the genes are annotated with the gene IDs from Ensembl instead of the ones from RefSeq. Nevertheless, I can still perform GO analyses...with Ensembl ID with a different program, but I need a list of the DE genes s…

GOanalyses edgeR DEgeneslist

updated 4.9 years ago • Rodrigo

<div class="preformatted">Hi Bioconductor Developers and Users, I'm using some of the Bioconductor packages to analize Illumina 450k data for identifying differentially methylated positions/sites and Genes associated with these ones. With the IMA package version 3.1.2, I've some lists as many as those annotated by it and these lists are indexed by the Genes Symbols/Names and then there ar…

minfi minfi

updated 11.7 years ago • Giovanni Calice

<div class="preformatted">Alex hi, I'm not sure whether you can directly prevent the hyperGTest function from testing small gene-sets. It tests all gene-sets as a default. However, you can certainly filter the list of significant gene-sets by set size. The summary() function for the test output has a "categorySize" argument. Suppose the output of your test is called "testresults". Then…

updated 17.8 years ago • Assaf Oron

I did GO enrichment analysis on all of the DE genes, up-regulated genes and down-regulated genes separately. Since over-represented (enrichment) are easy to understand...I want to know what is the biological significance of under-represented genes? Can I say under-represented genes have similar biological significance with over-represented (enrichment) down...regulated genes

go rnaseq clusterprofiler topgo

updated 8.2 years ago • Jack

Hi there, I'm seeking input on normalizing library depth across experiments to compare gene detectability at different time points. I have read count matrices for three experiments representing early, mid, and...time point data (older technology). I converted counts to CPM and determined the 10th percentile of genes detected in at least 50% of samples from these two time points. I then applied t…

DESeq2 Normalization

updated 6 months ago • Mara

the package, the TxDb object looks fine, but applying any function to it fails.  For example genes() gives character(0) and seqlevels() gives an empty GRanges object:     <pre> > library(TxDb.Hsapiens.UCSC.hg19.knownGene...gt; txdb = TxDb.Hsapiens.UCSC.hg19.knownGene # abbreviate > genes(txdb) GRanges object with 0 ranges and 1 metadata column: …

TxDb.Hsapiens.UCSC.hg19.knownGene

updated 8.3 years ago • l.selfors

a 'naive' question for you. I need to know if there is a good and broadly accepted way to select genes that are not differentially expressed in a microarray experiment. I am looking for a measure of the significance for...the potential 'not differentially expressed' call that could be given to a gene and that can be considered reliable from the community. I have searched the internet but found …

Microarray Microarray

updated 19.7 years ago • Mike Ferker

A/B annotation. However, I got very different results from the ones obtained when trying to compute gene density myself. Looking at `` pca.hic `` function, it seems that gene density is actually gene number per sign, whatever the

HiTC

updated 7.6 years ago • cath

v2) they added annotation with help > y <- DGEList(fc$counts, group=group) > y$genes <- fc$annotation[, "Length", drop=FALSE] How can I add `` rawCountTable `` into `` edgeR `` and tell it that the first column represet...the `` y$genes ``? Thank you in advance

edger

updated 8.3 years ago • mictadlo

start", "end"), values = list(chromosome, x1, x2), mart = biomart) then I would get a return of all genes that completely lie between x1 and x2. What I would like is all genes that overlap that region. Ideally I could do this by

biomaRt biomaRt

updated 17.3 years ago • Elizabeth Purdom

with just M1 and M2 conditions, and eventually more. I would also like to be able to choose the genes in this heatmap (if you have advises on how to do this, I'll take it !) So for now I have : 1. the AffyBatch form the CEL files 2. the...contrasts) From which one should I build the matrix for heatmap() ? How ? I want to focus on gene coding for plasma membrane proteins, is there a way to…

heatmap

updated 9.1 years ago • giroudpaul

by the differential expression I am seeing. It returns the pathway (GO Term), the percentage of genes impacted and the setSize. I want to find the other genes in the set. So say it give 60% of genes in a GO term with a set size of...100 are impacted, I want to know what the other 40 genes are. Is there a way to access the what is in the set for each GO term specific to gseGO? I can find a…

gseGO setSize

updated 3.3 years ago • Adelyn

div class="preformatted">Dear group, i want to convert all gene sets available from GSEA (C1,C2,C3 and C4) into a 4 different gene sets, so that I can use geneSetTest of limma on above 4 different...gene sets. In one of the examples (classic estrogen example, only one set is described). What kind of formats geneSetTest will...read for gene sets. ( e.g. every set writting in a single line f…

limma convert limma convert

updated 17.6 years ago • Srinivas Iyyer

Hello, I am compeletly new to gene expression in R. I want to install edge R, Limma and .... but when I try to install them it gives me an error which; # if (!requireNamespace

limma edgeR Biobase GeneExpression

updated 4.4 years ago • sogol.bouyeh

div class="preformatted">Hi all, >Comparing expression b/w genes (as opposed to across conditions for >a given gene) is not a standard use case within edgeR (yet) and >there are a number...differences in read counts that are different from gene to gene. Following up on this idea of the problems in comparing expression levels between different genes using RNA-Seq...these …

edgeR edgeR

updated 14.9 years ago • Jenny Drnevich

GBM", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - FPKM-UQ", barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005...save.filename = "exp.rda") ``` My question is: is there a way to filter for what genes we want to include in the…

tcgabiolinks filtering gdc TCGABiolinks rnaseq

updated 6.0 years ago • jam526

Hi! I would like some suggestions on filtering low variance genes for WGCNA. I have done a round of WGCNA exercises on my own RNA-seq data. I filtered out genes with low counts (less than 10...from the DESeq2 package, as recommended from the WGCNA FAQ page, and this gave me a total of 18303 genes (originally 30023 genes) for the network analysis. I got 14 nice modules, with the gene number…

deseq2 WGCNA

updated 6.0 years ago • minyaaa9058

div class="preformatted">Hi, Is there a function available on Bioconductor to convert gene symbol aliases to official gene symbols? Regards, Charity </div

convert convert

updated 17.5 years ago • Charity Law

and couldn't find a direct answer anywhere: Does it make sense to perform limma on only a subset of genes? An example: I am only interested in if there are differences in gene expression between the groups of interest in 700...previously defined genes that had been identified (by limma) in another independent experiment (using a different experimental technology...one could say it would make sen…

limma

updated 11.2 years ago • Simone

been slowly replacing `biomaRt` queries with the annotations in `ensembldb`. Basically to retrieve gene symbols, and gene locations, by querying with ensembl IDs. One thing that I could not find was how to retrieve "gene descriptions

biomaRt ensembldb AnnotationData

updated 4.8 years ago • António Miguel de Jesus Domingues

told me to do this kind of analysis. because he believes that if i randomly select 185 others genes among the 6000 i will have the same annotation results .... > Date: Mon, 4 Jun 2012 09:14:13 -0400 > Subject: Re: [BioC] Gene list annotation...wrote: > > > > Hi, > > I'm trying to measure the significance of my gene annotation list. >…

Annotation GO annotate limma GOstats topGO Annotation GO annotate limma GOstats topGO

updated 13.6 years ago • Stéphanie haaaaaaaa

Hi there, I wanted to extract the TSS up-stream region of each gene up to the end position (TTS) of the nearby gene. I only known the promoter function, but it seems can not deal with...this problem. I could only get the GenomicRange object of  all genes from the gtf file by the following codes:   <pre> txDB <- makeTxDbFromGFF("test.gtf…

genomicranges genomicfeatures promoter upstream_flank

updated 7.3 years ago • Wojeff

rnaseqGene/\#annotating-and-exporting-results) and had a question about the appropriate list of genes to use from the latest Gencode mouse comprehensive gene annotation (CHR) GTF/GFF3 file. The goal of this project is to perform...4.956042 -4.534543 5.772839e-06 9.728545e-03</pre> 4. Use the org.Mm.eg.db library to annotate the gene names corresponding to the gene IDs from the gff3 file. I…

deseq2 tximport org.mm.eg.db gencode

updated 7.8 years ago • pvd2107

Expression Analysis with DEseq2. I got my results (res) which contains lets say 100 rows of genes. Now I want to remove 5 genes (gene called "fg", gene called "gh", ...). I tried with "select" but it tells me that this function cannot...be used for DeSeq. How can i remove 5 genes in res? Thank you, Bine

deseq2 res

updated 5.5 years ago • Bine