Bioconductor Forum

82 matrix in which rows are the genes and col are samples respectively. I have to define templates using 6 different combination for which have used the following code; templates <- permutations(3,6,c(-1,0,1),repeats...c(17,18,19,20) com6 <- c(21,22,23,24) com7 <- c(25,26,27,28) To get the 729 profiles for the templates using permutation code is as follows profile &l…

updated 15.3 years ago • Harikrishnadhar

Hi, I tried to uploead my template but I'm having this error, do I need to had an especific format for ma Fasta file? > library(openPrimeR) There are missing...Hi, I tried to uploead my template but I'm having this error, do I need to had an especific format for ma Fasta file? > library(openPrimeR) There are missing/non-functioning external tools. To use …

PCRmultiplex openPrimeR

updated 2.9 years ago • Santiago Edilberto

<div class="preformatted">We are running experiments where there are technical difficulties in getting a pure template of interest. What we have is a mix of template-1 (our template of interest) and template-2 (the contaminating template). We have pure samples of template-2 that we run alongside the mix. We also run several HSK genes to use for normalization. Using HTqPCR, is there a wa…

HTqPCR HTqPCR

updated 12.6 years ago • Penny, Susanne

div class="preformatted">Dear group, Which package can get me the chromosome number and coordinates of that gene on the genome along with gene names. Is there any such package or function? Thanks

updated 21.2 years ago • S Peri

for monocytes and eventually HLA-DR tagged monocytes. What kind of information goes in the gating template? I am currently basing my template off an example template for lymphocytes, but I am sure some things need to be changed

opencyto gating

updated 8.5 years ago • justinyi10

div class="preformatted"> I found no of homology pairs in R homology package is different from http://inparanoid.sbc.su.se/download/current/table_stats/ For example...sapien-Spombe pairs in Hom.Hs.inp.db, inparanoid website claims, 5615 sequences H.sapiens.fa have homologs in dataset S.pombe.fa 2986 sequences S.pombe.fa have homologs in dataset H.sapiens.fa May I know did you apply...any cu…

updated 13.1 years ago • Guest User

Hi all, I tried to determine probesets of hgu133a which correspond to transcripts which are homologous to all rat transcripts measured on rae230a. I thought using the homology datapackage would be a good idea but didn

hgu133a rae230a hgu133a rae230a

updated 21.5 years ago • Claudio Lottaz

div class="preformatted">Greetings, In the vignette, "How to use the homology packages" under Task 1, what is the recommended method of obtaining the LocusLink IDs of the homologous genes? Sincerely

updated 20.8 years ago • Lynn Young

div class="preformatted">Greetings, In the vignette, "How to use the homology packages" under Task 1, what is the recommended method of obtaining the LocusLink IDs of the homologous genes? Sincerely

updated 20.6 years ago • Lynn Young

Hi everyone, I'm wondering where could I find the number of protein-coding genes in each chromosome arm in human? I have searched the ensembl, but it only gives the the number...of protein-coding genes in each chromosome instead if dividing with arms. Wondering if anyone could give any suggestions or if I could get the information

gene chromosome proteincodinggene

updated 2.7 years ago • Liliian

div class="preformatted">Dear list, I'm trying to obtain a list of mouse homologs of human genes present in Affymetrix chips (human hgu133plus2 and mouse 430) following the homology packages Vignette

hgu133plus2 hgu133plus2

updated 20.5 years ago • Bosotti, Roberta [Nervianoms]

class="preformatted">Hi everybody I have a list of entrezid of hsapiens and I am trying to find the homologs genes in zebrafish and xenopus laevis. using package BiomaRt, function getHomolog I was able to do oit for zebrafish

Xenopus laevis zebrafish biomaRt Xenopus laevis zebrafish biomaRt

updated 18.3 years ago • Mayte Suarez-Farinas

I have been trying to us goTools (but any other package would be fine) to produce gene category pie charts for arabidopsis genes. My gene lists are in the format AT3G12345 etc. but most of these could be mapped to GeneChip probesets

goTools Category goTools Category

updated 18.2 years ago • Naomi Altman

fhcrc.org> Date: Thu, Dec 24, 2009 at 5:35 PM Subject: Re: [R] Question to use R plot GO pie chart To: "Waverley @ Palo Alto" <waverley.paloalto at="" gmail.com=""> Cc: r-help at r-project.org Waverley @ Palo Alto wrote: > Hi, > &gt...whether there is a > package which can map the gene ontology to these IPIs, and plot the > pie chart to demonstrate the mo…

GO Cancer Category GO Cancer Category

updated 16.0 years ago • Waverley @ Palo Alto

Hi, I want to retrieve human and rat homologs from the Ensembl 107 archive and I get the following error: ```r mart_rat <- useMart(host='jul2022.archive.ensembl.org...Hi, I want to retrieve human and rat homologs from the Ensembl 107 archive and I get the following error: ```r mart_rat <- useMart(host='jul2022.archive.ensembl.org',biomart="ENSEMBL_MART_ENSEMBL",dataset="rnorvegi…

biomaRt ensembldb

updated 2.9 years ago • virginie.dubourg

This worked nicely but I would like some information on the alignment, specifically the percent homology between the different proteins? If possible percent homology to one of the sequences in particular. I.e. I really...want to align all the sequences to one "query sequence" and get a percent homology to that query sequence. Thanks   &nbsp

decipher r protein alignment

updated 7.7 years ago • reubenmcgregor88

I have successfully generated a dseq2 from the count matrix but I want to add the respective chromosome numbers to the gene ids in deseq2 output. I am working with Oryza sativa. How to perform the annotation and with which

NewWave hgu133a2.db

updated 2.3 years ago • roy23032

When trying to apply a gate in openCyto, however, the program adds the dims from my gating template as populations: > gt<-gatingTemplate("/Users/justinyi/Desktop/gating\_template.csv") Adding population:monocyte...gFunc\_args): failed at A1\_11.fcs Error in .find\_peaks(x, ...)\[, "x"\] : incorrect number of dimensions Here is my gating template. If someone could he…

opencyto gating

updated 8.5 years ago • justinyi10

When I try to gate from my gating template, I am hit with the following error. Why is this? My GatingSet only consists of 10 experiments Error in (function (fs, pp

opencyto gating

updated 8.5 years ago • justinyi10

Hello BC community, I am trying to convert a list of human genes to mouse homologs using R. Biomart finds homologs of some genes but not others. I can't seem to figure out the reason for this behavior

biomart homolog ortholog gene conversion ensembl

updated 6.2 years ago • atakanekiz

Hi all, I have several results of a CGH analysis, where a statistic is plotted vs the chromosomes length. Does anybody know if there's a way to plot a graphical representation of each chromosome, with the regions...it with my plot and directly compare which area of the plot corresponds to which region of the chromosome ? It would be great to have directly a way where i can impute the statisti…

CGH impute CGH impute

updated 16.8 years ago • Giulio Di Giovanni

8083415" "ENSG00000114771" which R package does the conversion of the list of IDs to find the Mouse homologs and can someone type the exact command? Thank you for your consideration. </div

updated 15.6 years ago • David Lyon

I'm working on gating my raw FCS files. I have successfully created a template that gates for monocytes. Now I am trying to identify HLA-DR+ monocytes from the previously gated monocyte population...the openCyto program keeps creating two populations that I've listed in my dims column of the gating template (see below). I was wondering if you could help me figure out why. I've attached my gating …

opencyto gating gating bioconductor

updated 8.5 years ago • justinyi10

I am trying to run the TCGAvisualize\_EAbarplot function, but instead of producing the expected charts it did this: ![](webkit-fake-url://e6a0cc2a-a60c-43c9-a26c-a163ec8c34b4/image.tiff) Any ideas why it didn't run and just produced

TCGA

updated 9.8 years ago • pgreylin

div class="preformatted"> Hi All, I have a question about analyzing aCGH data with huge number of probes on a single chromosome. We have a set of customized NimbleGen aCGH human sample data. Each sample has 40 million...probes. Even a single chromosome has >3M probes. I tried some R-based and Matlab-based aCGH analysis software to analyze just a single chromosome...If you have, can you…

aCGH aCGH aCGH aCGH

updated 17.8 years ago • pingzhao Hu

600 amino acid sequences in clustal format (or FASTA format too) with BLOSUM62 matrix to achieve homology score. We used pairwise alignment but we aren't able to compare our sequences with BLOSUM matrix because pairwise

Alignment Alignment

updated 14.0 years ago • erikafalisi@tin.it

wrote: > > > > Hi All, > > I have a question about analyzing aCGH data with huge number of > > probes on a single chromosome. > > We have a set of customized NimbleGen aCGH human sample data. Each sample...gt; > has 40 million probes. Even a single chromosome has >3M probes. > > > &gt…

aCGH aCGH aCGH aCGH

updated 17.8 years ago • pingzhao Hu

table in this style: "Chr1_1242_1625" where 1245 and 1625 are the start and end positions along the chromosome. I would like to obtain the peaks for just one chromosome for downstream analysis. Is there any way of subsetting...the results of DESeq2 by providing it with a chromosome number? I am reluctant to subset the dataset and just run the analysis on the single chromosome as I assume…

deseq2

updated 5.6 years ago • Charlotte

div class="preformatted">I am working with a number of bacterial genomes. I would like to define my own chromosome and annotations along the chromosomes, then view gene

geneplotter genomes geneplotter genomes

updated 20.7 years ago • Palmer, Lance

I am trying to find modifications in genomic location. Now, the output I am getting is in the chromosome and location of the modification (attached file). I am not sure how to convert it into a gene name using biomart or...this issue? Here I don't have a range of base pairs. However, as shown below, I have just a position number in a particular chromosome number. ![enter image description here]…

biomaRt ensembldb

updated 3.1 years ago • mbansal

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

Hello, I have a .tif file of a ranged bar chart, with the bars arranged vertically, representing the temperature ranges of nine different countries. I need to analyse

EBImage

updated 7 months ago • ekatcher

<div class="preformatted">Hi everybody, I was wondering if there was a simple function allowing me to do this, plotting a GO-output search from ensembl into a pie-chart? I looked at biomaRt but the main problem I'm facing here is actually calling ensembl database as my Institute doesn't...was a simple function allowing me to do this, plotting a GO-output search from ensembl into a pie-chart…

GO biomaRt GO biomaRt

updated 19.6 years ago • Celine Carret

I have to make the chromosome name to "4" rather "chr4" because my dataTrack 's chromosome names are numbers without "chr". I read the tutorial, and did...Ming  <pre> options(ucscChromosomeNames=FALSE) itrack<- IdeogramTrack(genome = "hg19", chromosome = 4) Error in .local(.Object, ...) : Chromosome '4' does not exist on UCSC genome 'hg19'</pre

Gviz

updated 10.4 years ago • tangming2005

updated to one of the last versions. Doing so, some gates stopped functioning from the gating templates, and few others were broken. Here is my take and how I corrected tmix to make it works, and I would also ask for some guidance...the filter seems not applicable to cytoframes, but only to flowframes. For my use in the gating templates, I took the code of gate_quad_tmix, and implemented the c…

filter gate_quad_tmix gt_gating

updated 3.8 years ago • Pierre

Hello I am using DiffBind for ATAC-Seq analysis. I would like to remove peaks located on random chromosomes and chrUn (Unplace Chromosome). I found the argument bRemoveRandom = T in the dba() function, nothing for chrUn. So I...Hello I am using DiffBind for ATAC-Seq analysis. I would like to remove peaks located on random chromosomes and chrUn (Unplace Chromosome). I found the argument bRemoveRa…

DiffBind

updated 16 months ago • mdidish

Hi, I feel the chromosome information is wrong in the output of the cpg.annotate command.  Could you check what's wrong here? > summary

DMRcate

updated 9.5 years ago • yuping.zhang

the package, but I'm running into an issue that i cannot seem to fix. It regards the usage of a CSV template to define the gating strategy. In this CSV file, I'm able to create relatively simple gates, but when i try to make a gate...and no further gating can be done on any of the quad gates as i cannot use them as parent in the CSV template due to the overwriting if the alias. So basically wha…

opencyto FlowCytometry

updated 3.2 years ago • Noël

div class="preformatted">Hi all, >From the output of a custom HMM routine, I have data showing chromosome number and nucleotide position, but no associated gene name or database identifier. e.g. > logRiList[[1]][1:10,] chromosome...3 10 1 320085 320085 0.7877 3 How can I map this data to RefSeq Accession number or EntrezGene ID etc. so I can get the name of …

Cancer Breast Cancer Breast

updated 16.7 years ago • Steven McKinney

I have generated a set of primers with openPrimeR, but I got only one set. How can I increase the number of sets returned byopenPrimeR, let's say to 10? Thanks ``` library("openPrimeR") fasta.file <- system.file("extdata", "IMGT_data...templates", "Homo_sapiens_IGH_functional_exon.fasta", package = "openPrimeR") # Load the template sequences from 'fasta.file

openPrimeR

updated 4.8 years ago • marongiu.luigi

I am trying to read in a gating template I created (.csv) using the following commands, however I am hit with an error. gtFile<-system.file("/Users/justinyi...I am trying to read in a gating template I created (.csv) using the following commands, however I am hit with an error. gtFile<-system.file("/Users/justinyi/Desktop

opencyto gating bioconductor

updated 8.5 years ago • justinyi10

working very well for me. However, I have discovered that analyzeChr() is still having issues with chromosomes > 22. When I give it a chromosome in the human range, it does fine, but once we get up into higher numbers, it breaks...ifelse(grepl(filename, tameFileNames), "tame", "aggr") })) # Initial data analysis over all chromosomes: print("Starting fullCoverage...") fullCov <-…

derfinder

updated 11.1 years ago • jessica.hekman

class="preformatted">Hi group, I am interested in retrieving about 2000 sequences with the specific chromosome number,start and end site. I was thinking of using BSgenome package for this. >source("http://bioconductor.org/biocLite.R...this would work for specific values. #So I tried to use a dataframe where it would retrieve chromosome number from by using >full<-as.mat…

BSgenome BSgenome BSgenome BSgenome

updated 14.4 years ago • viritha kaza

the Variation page into Variation (Germline) and Variation (Somatic) * Renamed "chromosome\_location" internal name to "chromosome\_start" and added a new attribute called "chromosome\_end" in the Variation...new attribute called "somatic\_chromosome\_end" in the Variation (Somatic) page * Renamed "Chromosome Location (bp)" attribute to "Chromosome position start (…

biomart ensembl release news GRCh37 News

updated 10.8 years ago • Thomas Maurel

Desktop/08272014/IDATs") As confirmation that all of the features were imported, I checked the number of rows in methyLumiSet: <pre> nrow(methyLumiSet) Features 485577</pre> The methyLumiSet is based off of the eSet class...fall on the Y chromosome using the following code with the idea that I would then remove those probes from the methyLumiSet. <pre> methyLumiSet.C…

methylumi eSet illuminahumanmethylation450k.db featureFilter

updated 10.5 years ago • martens.christopher

range. For example, using following code could retrieve snps between 10000 to 20000 basepair on chromosome 2. ####====================== library(rtracklayer) browserSession("UCSC")->session ucscTableQuery(session, "snp129",GenomicRanges(10000...is how to retrieve data using identifiers(names/accessions). for example, is it possible to retrieve chromosome position given the rs number of se…

rtracklayer rtracklayer

updated 16.5 years ago • li lilingdu

appreciate any suggestions/remarks regarding available BioC packages that display as heatmaps the chromosome-to-chromosome/gene-to-gene interactions. thank you , bogdan [[alternative HTML version deleted]] </div

updated 12.3 years ago • Bogdan

I want to use "BatchtoolsParam" to parametrize schedule options on _slurm_ backend. When using slurm backend, the template `` slurm-simpl.tmpl `` provided by batchtools is used to parametrize `` sbatch `` variables. My problem is that I cannot find a way to pass the `` resources `` variable to the template; Here is my code: <pre><code class="language-r">library(BiocParallel) piAp…

biocparallel BatchtoolsParam

updated 7.2 years ago • Chao-Jen Wong

I am interested to obtain the curve line graph with the ribbons as described here. [Line chart with error envelop: ggplot2 and geom_ribbon()][1]. However, I do not see this pattern. Please assist me with this. I have attached

ggplot2 line chart R geom_ribbon()

updated 6.2 years ago • mohammedtoufiq91

But for the copy number variation, I get only chromosomal locations. To do the PCA, I want to have a table with gene, expression by sample, CNV by...of my CNV dataset with a gene, but the final result in masked.dt is completely incoherent (ie the chromosomal location retrieved with TCGA biolinks package do not match those of the genes I retrieved with Biomart. Could...lt;- GDCquery(project = "T…

TCGAbiolinks biomaRt

updated 2.6 years ago • Will Yam

Hi, I am trying to convert "chromosome postions" to "hgnc_symbol" using R. I referred the below site. http://statisticalrecipes.blogspot.com/2012/08/biomart...chromosome_name, start, end listFilters(mart) # Read in tab-delimited file with three columns: chromosome number, start position and end position positions <- read.table("positions.txt") # Extract HGNC gene symbol …

microarray

updated 6.1 years ago • joyk2a

like to get the counts "per gene". The code runs successfully and I get an output table, but the number of records in the output table are ~57000: cat count.tsv | wc -l 57774 I am wondering why the number of counts are so much greater...than the total number of genes (~30,000). I am getting some warning message, which may be related to this, especially #1 and #4: Warning messages: 1...filesDi…

GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt

updated 11.7 years ago • Guest User

would be grateful for your advice as my R level is a bit basic and I got stuck. I need to count the number of reads per gene and my fastq data was aligned to chromosomes named "1", "2" etc. while makeTranscriptFromUCSC provided...chromorome names returned from the make that the TranscriptFromUCSC (or if available the full gene) chromosome names will not include "chr" (or any way that they would m…

Cancer TranscriptDb convert Cancer TranscriptDb convert

updated 13.9 years ago • Hervé Pagès

How to remove extra chromosomes like chrUn\_gl00\* from pairParam object. Error in preparePairs("/Users/thimmamp/temp\_tobe\_deleted/HiCMapped..._presplit\_out\_fixmate.bam",  :   conversion table should have length equal to the number of chromosomes > str(hs.param) Formal class 'pairParam' \[package "diffHic"\] with 4 slots   ..@ fragments:Formal cl…

diffHic

updated 9.4 years ago • manjulathimma

via R package biomaRt. I wanted to download all ensembl transcripts from the entire mouse genome (chromosome 1:19, X, Y MT only). When I set the filter based on chromosome names I retrieved ~36000 transcript, please see the code...using the web service www.biomart.org I received ~48000 transcripts for the same genome version and chromosomes. By comparing these two data frames you could see that…

Annotation biomaRt Annotation biomaRt

updated 16.2 years ago • Ivanek, Robert

of issues. First,the ensemble-based gtf file that I used to align all my mouse RNAseq data has the chromosomes named as “1, 2 , 3”… Rather than “chr1 , chr2 ..”. My Testing R code for summarizeOverlaps is as follows:   <pre> library(TxDb.Mmusculus.UCSC.mm10.ensGene...the mm10 sqlite I am using has chr1, chr2 .. Format seqinfo(bamLst_grp1) #this shows that the chromosome names…

summarizeoverlaps RNAseq annotation counts

updated 10.0 years ago • bioprog

range. For example, using following code could retrieve snps between 10000 to 20000 basepair on chromosome 2. ####====================== library(rtracklayer) browserSession("UCSC")->session ucscTableQuery(session, "snp129",GenomicRanges(10000...is how to retrieve data using identifiers(names/accessions). for example, is it possible to retrieve chromosome position given the rs number of se…

rtracklayer rtracklayer

updated 16.5 years ago • li lilingdu

you of the incorrect use of the term "ortholog". The term "ortholog" is a special type/subset of "homolog", as too is "paralog". When talking about genes, these terms describe what we know about the evolutionary history of a...Homologous genes are related to each other by having the same common ancestor. Homologs can be further divided into orthologs...and paralogs (among others which are more c…

annotationTools annotationTools

updated 17.5 years ago • Nathan.Watson-Haigh@csiro.au

div class="preformatted">Hi, I'm wondering to how updated hom.Hs.inp.db is. "Title: Homology information for Homo Sapiens from Inparanoid" According to the title of the package, the data is from Inparanoid

GO Homo sapiens GO Homo sapiens

updated 13.4 years ago • Peng Yu

preformatted">Hello, I'm trying to run the MEDIPS package with the following script (loop over each chromosomes, compare each conditions ) https://gist.github.com/lindenb/6297130d57146ec2c2c0 everything works fine for...as log2(MSet1/MSet2). Creating results table... Adding differential coverage results... Total number of windows: 5701362 Number of windows tested for differential methylation…

Coverage Regression edgeR MEDIPS Coverage Regression edgeR MEDIPS

updated 12.0 years ago • Pierre Lindenbaum