Bioconductor Forum

preformatted"> Dear all, I'm using GOSemSim for computing semantic similarities (semsim) between clusters of genes. The Problem: I'm obtaining semsim==NA when comparing clusters of genes from which I actually expect a value...i.e. semsim != NA). However, if I compute semsim between individual genes (present in the analyzed clusters) I obtain semsim values != NA. For computing semsim between…

GO SemSim GOSemSim GO SemSim GOSemSim

updated 11.8 years ago • Guest User

I have already converted my gene names to Entrez IDs and used pathview to map appropriate genes to my pathway of interest. How do I figure out which of my...genes mapped to a specific node? Please, let me know if I can clarify anything. It's my first time doing pathway analysis, so I would

pathview

updated 7 weeks ago • Julie

has a new structure/content. Modules (to be covered at a rate of approximately 3/day): *Taster: Gene expression in airways hyperresponsiveness; annotation, gene set enrichment; transcript profiling in the yeast cell...spikein data and comparison of preprocessing methods; affyPLM; affylmGUI; other technologies *Gene filtering: mechanics: closure of exprSet class under subsetting; su…

Annotation GO Preprocessing Clustering Yeast probe RSNPper biomaRt Annotation GO Yeast

updated 17.9 years ago • Vincent J. Carey, Jr.

to NA values or ?no mapped data?. If you haven?t, pathview will install the "org.Mm.eg.db" package, which is needed for mapping the gene symbol to...gt; kegg.names labels type x y width height mol.data mol.col > 1 1029 CDKN2A gene 532 124 46 17 0.1291987 #BEBEBE > 2 51343 FZR1 gene 919 536 46 17 -0.4043256 #5FDF5F > 3 4171 MCM2 gen…

pathview pathview

updated 10.8 years ago • Luo Weijun

Dear all, please may I ask for a suggestion regarding the algorithms to cluster the expression data in single cells at multiple time points : we do have 10 scRNA-seq datasets that have been collected...time points, and we have done : -- the standard scRNA-seq analysis in order to identify the cluster specific markers and -- the standard scRNA-seq analysis in order to identify the …

scRNA-seq time series

updated 3.9 years ago • Bogdan

I am analyzing CNV data downloaded from TCGA database (level 3) and aim to convert it to a gene-level matrix. The files are like the below: <pre> Sample Chromosome Start End Num_Probes Segment_Mean BAIZE_p_TCGA_b138_SNP_N_GenomeWideSNP_6_A02_808774...1 17764034 221905958 105172 -0.0073</pre> To convert CNV data to gene-level data, I map genome regions t…

TCGA CNV

updated 9.0 years ago • NS

Hi, I have a group of genes upregulated in various clusters of cells when I run Seurat's FindAllMarkers() function. Is it statistically correct...to use run compareCluster::compareCluster() on a list of these upregulated genes grouped per cell cluster? Or must the genes be grouped per GO before running compareCluster(). Thanks in advance for your

clusterProfiler bioconductor

updated 3.8 years ago • charlesgwellem

div class="preformatted">Hi, I was trying to map clone IDs to gene symbols for microarray data. I looked at the org.Hs.eg.db package, but this doesn't appear to have the mapping. Or should

Microarray Microarray

updated 15.5 years ago • Tim Smith

div class="preformatted">I have a general question about clustering of genomic data. The heatmaps that are generated are usually scaled row-wise so that variations are apparent...documentation of heatmap and hclust, however, is appears that this scaling is done after the actual clustering is performed. If heatmap is performed on the hclust object with scale="none", it is apparent that most of …

Clustering Clustering

updated 18.2 years ago • Kimpel, Mark W

Hello Sir/madam, I'm using R to plot a heatmap of Differentially expressed genes of microarray data and RNA seq data. i have used heatmap.2 of gplots to plot the heatmap. My question is, 1. now i want to extract...Hello Sir/madam, I'm using R to plot a heatmap of Differentially expressed genes of microarray data and RNA seq data. i have used heatmap.2 of gplots to plot the heatmap. My ques…

heatmap.2 hierarchical clustering microarray RNA seq DEG

updated 6.2 years ago • lawarde.ankita1

div class="preformatted">hello friends during k means clustering when i am trying to test total no of possible clusters with th foowing code error is coming as follows: kmax<-c(100

Clustering Clustering

updated 13.0 years ago • Budhayash Gautam

Agilent-034879 ADchip_1.0 033934 (Probe name version) In the above GEO Series, I have extracted top genes for differential expression analysis. Some of the IDs are as follows: ACUST_8984_PI426217866, ACUST_4639_PI426333075...ACUST_4167_PI426418842 Is there any Bioconductor package to convert these probe IDs to gene names or symbols? DAVID and g:Profiler gave no results

AgilentChip

updated 2.1 years ago • Prateek

microarray dataset (https://support.bioconductor.org/p/68307/\#69270), i have acquired __5 DEG gene lists representing unique genes found DE between each specific biological treatment implemented vs the control group...DMSO)__. As i want to perform some unsupervised machine learning such as clustering and a possible heatmap of the intensities of these genes, im wondering how i should proceed base…

heatmap.2 clustering common DEG genes bioconductor

updated 8.9 years ago • svlachavas

div class="preformatted">I have an expression matrix confined to the genes I wish to plot e.g. sample1 sample2 ... gene 1 gene 2 ... This may be a simple question, but is there a single command to do gene expression...Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW…

Cancer Cancer

updated 17.2 years ago • Daniel Brewer

experiment comparing two strains of rats, I have a list of about 200 significant affy rat probesets (genes) that I have mapped to their chromosomal locations. Some of the genes appear to cluster into discrete physical chromosomal...genetic differences between the two inbred strains. Based on their chromosomal location, I have clustered these significant genes into discrete bins. Something thing t…

GO affy ASSIGN GO affy ASSIGN

updated 19.4 years ago • Kimpel, Mark W

expression analysis on some RNA-Seq data using limma, I’m trying to apply the [camera][1] method for gene set testing. I want to use gene sets from [MSigDB][2]. Unfortunately, as far as I’m aware, those gene sets are only available as...HGNC gene symbols (e.g., IDS) or Entrez identifiers. My RNA-Seq reads were mapped to ensembl gene identifiers (e.g., ENSG00000010404...I tried converting my ensem…

limma camera gene set testing ensembl

updated 4.4 years ago • Jeremy Beales

for *S japonicus*. I noticed that while Orthology.eg.db is able to convert most *Scomber japonicus* genes to NCBI Gene IDs, it fails to map LOC genes between species. For my analysis, I don't necessarily care that these genes aren...t actually orthologs and that in both species these genes are LOC genes. I am just interested in programmatically converting my genelist of NCBI Gene IDs between the…

Orthology.eg.db

updated 11 weeks ago • Benji Bromberg

div 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...1622894_at CG15120 FBgn0034454 37248 protein binding I would like to try and group the genes in various GO categories, which are mentioned here in th…

Annotation GO Annotation GO

updated 13.4 years ago • Assa Yeroslaviz

With `dba.plorProfile` function I can calculate the profiles but while plotting, I get the following error: ```r > profiles <- dba.plotProfile(dbobj, sites=overlaps) Generating...profiles... > dba.plotProfile(profiles) Plotting... Error in heatmap_width_pt * raster_quality : non-numeric argument to binary

DiffBind

updated 2.4 years ago • bhanu.chandra1

div class="preformatted">Hi, How can I cluster GOTerms and assoiciated number of genes from my prob set ids? something like: e.g. GOTERM Number of Genes associated...I have done something like below with my D E genes: Diff_MF <- makeGOGraph(myDiff_Genes,"MF","moe430a"); Diff_MF_nodes = nodes(Diff_MF); I have got terms below: MF_TERMS <- l…

GO GO

updated 19.6 years ago • Saurin D. Jani

<div class="preformatted">Hi, I am using Zebrafish Gene 1.1 ST Array Strip, I have found some transcript clusters that are differentially expressed but are not annotated (although they belong to the "main" design of the array). I would like to blast them, but I am not sure what to blast as each transcript cluster has various probes associated. Should I blast them all individually? I have r…

zebrafish zebrafish

updated 10.7 years ago • Joao Sollari Lopes

preformatted">Dear list, I've read the illuminaHumanv4.db.pdf, and it's not clear to me how the mappings are built. From the short package description, I thought the RefSeq ID's from the illumina array manifest would be...the ACCNUM is derived (from ?illuminaHumanv4ACCNUM: "For chip packages such as this, the ACCNUM mapping comes directly from the manufacturer."). I raise the question, since …

Cancer Homo sapiens Cancer Homo sapiens

updated 12.6 years ago • Mark Cowley

and patient IDs which satisfy the following conditions: __Whole exome sequencing + DNA methlation profile (450k) + Gene expression profile (RNA-seq)__ Is it possible to submit a comprehensive query for such a request, without

tcgabiolinks tcga genomicdatacommon

updated 5.7 years ago • franceschini.gianmarco

Hi I have several questions and I appreciate for answer : 1- I wanted to know how can I add cluster analysis like below image based on read count.   2- Should I run the code only for the genes with minimum number of...reads (e.g rowSum(gene) > 10) or I should run it only for DEGs ? Tnx.   <img alt="" src="https://i.postimg.cc/4dQ4rqMb/cut_tree_60pct_gene_cluster…

deseq2 rnaseq R

updated 5.6 years ago • ahmad.moousavi

I have some Waters raw files in profile mode and I can't convert them to centroid. I already tried to use the proteowizard and, unfortunately, it continues...I have some Waters raw files in profile mode and I can't convert them to centroid. I already tried to use the proteowizard and, unfortunately, it continues as...a profile. Does anyone know another way to perform this conversion from profile…

MassSpectrometry xcms

updated 3.5 years ago • dneu1002

I obtained several clusters and now I want to perform functional analysis to explore associated functions of the gene groups of interest. But...I had only the list of genes and the cluster. **How can I exctract data (Fold Change, pvalue etc...) regarding specifical cluster genes from my DESeq2 results...test = "LRT", reduced= ~1) res_LRT <- results(object = dds_LRT, ) # Subset results for…

DESeq2 RNASeq DEGreport

updated 3.2 years ago • Giulia

div class="preformatted">Dear list, I have some microarray data in which gene expression was profiled in two different tissues, collected at the same time from the same subjects. I would like to use...hierarchical clustering initially to cluster the gene expression patterns separately for each tissue. Then I would like to correlate...gene expression traits between the two tissues, and plot …

Microarray GO Clustering Microarray GO Clustering

updated 13.5 years ago • abosco@email.arizona.edu

a question about annotation. While annotating data with pd.clariom.d.human, I had a problem with genes that mapped to the same probe. If I annotate with this package, R takes only the first of the multiple genes. Even if I use...but this package caused an issue of a different kind: some probes were mapped to more genes than they should be. I realised this when comparing my results with Transcr…

clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human

updated 2.0 years ago • amir.rakhimov.b

Hello everybody, I have a trouble with the analysis of a ribosome profiling. I want to do de ratio of ratios of RFP an TOTAL RNA between two genotyopes. I do more or less the same as in this post...Hello everybody, I have a trouble with the analysis of a ribosome profiling. I want to do de ratio of ratios of RFP an TOTAL RNA between two genotyopes. I do more or less the same as in this post…

deseq2

updated 5.1 years ago • frene

div class="preformatted">Hi all i am using the following command to do clustering using hopach ....and getting the following erro .... eset.s is a matirx containing genes filtered through a ttest > gene.dist...known as Allahabad Agricultural Institute - Deemed University) Allahabad, UP, INDIA - 211 007 Ph. No. 9839845093, 9415261403 e-Mail rohit.farmer@gmail.com Blog http://rohitsspace…

Clustering Clustering

updated 14.0 years ago • Rohit Farmer

to normalize Affymetrix data (RMA, MAS5.0, and Li and Wong methods). I want to use hierarchical clustering method to cluster the normalized data according to experiments and genes. What would be a good software to use...I have used Dr. Eisen's "Cluster," but I got an error message. Thank you in advance. Shizuka</div

Clustering Clustering

updated 20.6 years ago • s0uchi02

Hi all,   Could anyone can help me to create mapping data file format used in OmicCircos. I want to make "mapping data file" for my expression data. I have a set of genes for...which I got chromosome start and chromosome end position. As mentioned in OmicCircos the mapping data file have chromosome position ( "Po") , I tried to get it for my set of genes but couldn't get it. …

omiccircos

updated 9.2 years ago • abdul rawoof

Hello, I just had a quick question about what "counts" is in ClusterProfiler. I am doing a project looking at functional enrichment of gene sets, and getting a graphical output using GSEA. I am just not sure what "counts" means in the graph that we get as a result. Here...about what "counts" is in ClusterProfiler. I am doing a project looking at functional enrichment of gene sets, and getting a g…

enrich clusterProfiler

updated 12 weeks ago • mpluchs

it took longer than I originally thought to add an option to Rsubread to make it output multiple mapping locations for multi- mapping reads. It has just been implemented in Rsubread 1.11.1 in Bioc devel branch. The 'nBestLocations...of Subread aligner (http://subread.sourceforge.net) straight away to get multiple mapping locations for multi-mapping reads. We have tested the new versions of thes…

Annotation Rsamtools Rsubread Annotation Rsamtools Rsubread

updated 11.1 years ago • Wei Shi

through this technique have both increased and diversified. Initial interest was focused on genes co-expressing across sets of experimental conditions, implying essentially the use of clustering techniques. More...note of caution. Design of experiments. Data preprocessing and normalization. Unsupervised analysis (clustering). Supervised analysis (gene selection, predictors). Functional profiling.…

Microarray Annotation Normalization GO Visualization Classification Clustering Survival GO

updated 16.3 years ago • Ana Conesa

preformatted">Dear BioC, I am working on ChIP-chip / ChIP-Seq data and I would like to do average gene mapping using absolute instead of relative coordinates. Does anyone have some idea or knows a package to do this ? In more...to do a plot of different histone modification enrichments (from WIG files) on a composite average gene using absolute coordinates like in PMID 17679090. In general p…

updated 14.2 years ago • Droit Arnaud

class="preformatted">Dear all, In the Affymetrix annotation file, I find that some probe set ID are mapped to multiple genes separated by '///', such as 200012_x_at is mapped to RPL21P16///RPL21P119///RPL21. How to handle this case? Thank

Annotation probe Annotation probe

updated 10.8 years ago • Feng Tian

isoforms, in alternative splicing differential expression. I would like to compare coverage profiles of the same isoform with or without the presence of the other isoforms, there is any tool, in bioconductor, that allows...manipulation of coverage profile, e.g. subtraction of a profile to an other or comparison between different coverage profiles? Cheers Raffaele -- ----------------------------…

Coverage Coverage

updated 10.7 years ago • rcaloger

function in EdgeR for pairwise comparisons of 3 conditions. I now want to make a union of these genes and cluster the expression (preferably, using the k-means algorithm). Following that, I would like to plot the expression...profiles of the clusters for the different conditions. I attempted doing this using ConsensusClusterPlus but I am unable...to interpret the tracking plot. I have…

EdgeR clustering differential gene expression consensusclusterplus kmeans

updated 6.1 years ago • anupriya.dalmia

div class="preformatted">Hi, could someone please help with Diana clustering and visualisation. I would like to do 1-way (genes only) and 2-way (genes and samples) clustering and visualise as a heatmap

Clustering Clustering

updated 19.4 years ago • Anthony Bosco

through this technique have both increased and diversified. Initial interest was focused on genes co-expressing across sets of experimental conditions, implying essentially the use of clustering techniques. More...note of caution. Design of experiments. Data preprocessing and normalization. Unsupervised analysis (clustering). Supervised analysis (gene selection, predictors). Functional profiling.…

Microarray Annotation Normalization GO Visualization Classification Clustering Survival GO

updated 16.5 years ago • Ana Conesa

<div class="preformatted">On Mon, May 3, 2010 at 8:39 AM, varpal singh <gilvarpal@gmail.com> wrote: > Respected Sir, > > I'm varpal singh, I'm writting to express my interest in clustering. > According your suggestio I got some good results with bioconductor. Now I > have got 847 genes after criteria (P value 0.05 and fold change -1><…

Clustering ctc Clustering ctc

updated 14.0 years ago • Sean Davis

Hi,  I am wondering how the result of GSEA using cluster profiler is different from that of GSEA GUI java application. I initially used GSEA GUI desktop application and tried...gseKEGG function. I assigned latest kegg database available online and pvalue cutoff of 0.05 for cluster profileR. I also assigned the same permutation number and minimum geneset size to be using the same conditi…

clusterprofiler gsea

updated 6.6 years ago • sup230

preformatted">hi there I am using R1.9.1 under mac OSX on an Apple iBook 640MB ram I'm trying to cluster my genes, and run into a memory problem (or at least, that's what it looks like). When i do: >single.clust<-function(d) hclust...col=pal, zlim=c(-3,3), scale="none", labRow=NA) I get a nice dendrogram if the kdata contains 10 genes, but it fails if kdata contains 1300 gen…

Clustering Clustering

updated 19.5 years ago • Floor Stam

Expression analysis of the three treatments versus the non-treated sample (NT), and I would like to cluster the DE genes in groups of genes that respond similarly to the three treatments and genes that only respond in one of...13 length(rownames(Filtered_AllvsCtrl$table)) [1] 2705 7- Plot data heatamp to cluster genes by expression pattern (here is where I cannot isolate the gene g…

edger complexheatmap R clustering

updated 4.0 years ago • eggrandio

I am not making a comparison between samples. Therefore, the result file shows the methylation profile for only one sample. In this results file, I noticed that the data is organized as such: chr start stop CF Ca2_MAPQ20.bam.counts...of 'coupling factor' is correct? 2) This lead to question how or what MEDIPS defines as a "region or cluster"? That is to say, on Chromosome 1, I have …

Sequencing MEDIPS

updated 9.6 years ago • Guest User

div class="preformatted">Hello, I'm interested to read about your experience using hierarchical clustering and dendogram visualization (via hclust) for several (cross chip) normalized chips. I'm not running the clustering...on all the genes on the chip. I select those genes that are significantly effected by the factors of interest (e.g. dose+time) via a linear...replicates, to reduce the nu…

Visualization Clustering Visualization Clustering

updated 20.1 years ago • Arne.Muller@aventis.com

I’m using topGO a lot for GO analysis and I’m worrying about the accuracy of the genes to GO terms mapping As an example, 2600+ genes are associated with a given GO term (e.g "GO:1903561”, Extracellular vesicle...using the topGO annFUN.org mapping and the org.Mm.eg.db database. When manually searching in the org.Mm.eg.db database, I get only 49 genes which is...set.seed(1234) require(org.Mm.eg…

topgo go org.mm.eg.db

updated 6.3 years ago • lehallib

To the developers,   I'm a novice R user and new to the expression profiling analysis as well. I am trying to do a differential expression analysis on a 2x2 factorial experiment (2 drought...To the developers,   I'm a novice R user and new to the expression profiling analysis as well. I am trying to do a differential expression analysis on a 2x2 factorial experiment (2 dro…

deseq2 rlog transformation

updated 6.3 years ago • tarun2

2 0.23</pre> How can I map __Tag__ to RefSeq ID or gene symbol? My goal is making a matrix of expression profile. Unfortunately, I did not find any useful information in [GPL9115

rnaseq EST gene Id

updated 8.5 years ago • NS

While doing the gene mapping from Affymatrix ids, I found out that there are multiple affymetrix IDs corresponding to a single gene name for...While doing the gene mapping from Affymatrix ids, I found out that there are multiple affymetrix IDs corresponding to a single gene name for a sample. My work revolves around gene names only. Please suggest the appropriate step to deal with this situation.…

biomaRt

updated 5 weeks ago • Reeya

<div class="preformatted">Hi, I build an annotation package for a mouse IPI database using "AnnotationDbi" (IPI.MOUSE.3.37.20080509.db) and am now putting it to use. I have a bunch of IPI-ID clusters ("SubjectiveClusters") each of which I want to check for GO terms significantly enriched over the combined set. I attached what I do, but was wondering whether ther's ways to do this without h…

Annotation GO Annotation GO

updated 16.0 years ago • Johannes Graumann

output\_file="alignResultsPE\_1.BAM",phredOffset=33 ) This also run succesfully, however, I get 0 mapping! And am abit concerned because I have no reason to believe out of ~300 samples that cell sorting has not worked correctly...of cells of interest, and the gating is stringent based on negative control samples... so I have no reason to doubt that these cells are not green!!..  Are th…

rsubread alignment align

updated 5.4 years ago • A

Guido wrote: > Dear list, > > Because I like the undelying idea, I have began using the re-mapped CDF files provided by the MBNI. However, triggered by a remark made by Dr MacDonald "... note that there are some downsides...the number of probes that map to a probe set for both default Affymetrix CDF file and Entrez-gene based re-mapped CDF file for the Mouse430_2 array. &…

Microarray Clustering cdf probe affy affyPLM mmgmos Microarray Clustering cdf probe

updated 17.3 years ago • Richard Pearson

effect as an element in the design matrix in EdgeR and it works perfect. I also want to make a clustered heatmap from the genes that were found to be differentially expressed. When I do this, the batch effect is visible...heatmap(logCPM_no_batch)</pre> The results look absolutely fantastic. Samples from the same batch no longer cluster at all, yet the basic appearance of the heatmap is th…

limma removeBatchEffect heatmap clustering

updated 8.3 years ago • Ekarl2

the ideas presented by P. Toronen in his BMC Bioinformatics paper: "Selection of informative clusters from hierarchical cluster tree with gene classes" 2004, 5:32 Before starting I would like to know if there have been

updated 16.9 years ago • Ariel Chernomoretz

Hello Bioconductor community, I have been struggling to find the answer for my analysis. I have two files for the data: one is an Excel file (including time points and the names of the samples, such as "stimulated vs. non-stimulated" controls), and a text file containing gene expression data (RNA-seq). The analysis should be longitudinal because we have a sample size of 25 participants, each w…

DESeq2 ctsGE

updated 8 weeks ago • Emma

the methylation data is soooo slow for being runned in my PC, so I need to run this script in a HPC cluster using the Slurm Workload Manager (this HPC uses MPI), but I had no idea about how to do it. Any suggestion? library(MethylMix...file = paste0(targetDirectory, "MET_", cancerSite, "_Processed.rds")) # Downloading gene expression data GEdirectories <- Download_Ge…

methylation epigenomics slurm mpi methylmix

updated 3.8 years ago • parra.sev

Hi everyone I want to know for cluster analysis of illumina microarray gene expression data (in idat format) which all the algorithms are used and which

clustering illumina microarray

updated 8.2 years ago • kritikamish99

RNAseq reads from an allopolyploid organism. This means that I will have groups of 2,3, or even 4 genes with high sequence homology among them. I am sure some reads will map to more than one gene. So far, my pipeline is 1. Map reads...to genome using tophat2, with default options (i.e., no -M or -g) 2. count using htseq as htseq-count -m intersection-strict --stranded=no --idattr=Na…

deseq deseq2 edger tophat bowtie

updated 8.9 years ago • ysdel