Bioconductor Forum

probably in the archives). When calling the makeVennDiagram function you want to set the totalTest number to something that is larger than the experimentally determined peak number. As far as I know, the totalTest number is...by chance. So one way to sort this out using biological information is to think about the maximum number of possible binding events and use that as the totalTest number. …

ChIPpeakAnno ChIPpeakAnno

updated 15.1 years ago • Noah Dowell

Now the problem within the gene_assoc > part is that there are genes which are not on the same chromosome as > the respective probs e.g. > > fsetid man_fsetid chrom physical_pos strand cytoband > 650443 CN_618877...downstream // 8981 // > Hs.524630 // UBE2N // 7334 // ubiquitin-conjugating enzyme E2N (UBC13 > homolog, yeast) /// NR_002212 // exon …

SNP Annotation PROcess SNP Annotation PROcess

updated 14.0 years ago • Benilton Carvalho

mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") ideogram <- makeIdeogram(chromosome = 7) genomeAxis <- makeGenomeAxis(add53 = TRUE, add35 = TRUE) gdPlot(list(ideogram, genomeAxis), minBase = 13730853, maxBase...14031050) I get a template with the idiogram and an axis of the area of intrest. How can I add the paired reads to that template (drowing rectangles

idiogram GenomeGraphs idiogram GenomeGraphs

updated 16.1 years ago • Ramzi TEMANNI

pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|6|0| 0 maker-Contig11328-pred_gff_augustus_masked-gene-0.0-mRNA...pred_gff_snap_masked-gene-0.0-mRNA-1 transcript Name:"Similar to dip2ba Disco-interacting protein 2 homolog B-A (Danio rerio)" offset:0 AED:1.00 eAED:1.00 QI:0|0|0…

Normalization a4 Normalization a4

updated 12.0 years ago • Guest User

div class="preformatted">Dear list, As I have read I can find chromosome number (using org.Hs.egCHR) , chromosome location (org.Hs.egCHRLOC) and end position(using org.Hs.egCHRLOCEND

updated 13.2 years ago • Fatemehsadat Seyednasrollah

div class="preformatted">Hi , I would like to get some inputs on analyzing copy number variants for a case control study. I have never worked with copy number variants before and I was wondering if there...are any R packages out there for analyzing copy number variants data and to get me started. I do have cell files from Affymetrix for my cases and controls. I appreciate your

updated 15.7 years ago • Kay Jaja

a step of a CNV analysis on cancer genomes, I would like to be able to COUNT and DISPLAY along the CHROMOSOME AXIS the NUMBER of READS in 10KB REGIONS of GERMLINE and CANCER GENOMES. I would like to ask you please for your suggestions...windows ? (possibly with Rsamtools ... ) -- a package/function that DISPLAY the COUNTS along the chromosomes ? many thanks, bogdan

read counting CNV rsamtools

updated 7.8 years ago • Bogdan

<div class="preformatted">Dear List, I wonder how to load RangedData for all chromosomes in a SINGLE tab in UCSC browser using browserView from rtracklayer. Currently, if I have a GRanges object for "mm9...div class="preformatted">Dear List, I wonder how to load RangedData for all chromosomes in a SINGLE tab in UCSC browser using browserView from rtracklayer. Currently, if I have a G…

rtracklayer rtracklayer

updated 13.6 years ago • Yue Li

div class="preformatted"> Dear Bioconductor community, I am looking for a package for Copy number analysis using CEL file that I have obtained from Affy SNP 6.0. I have CHP files from birdseed. Now I want to analyze my...data for Copy number and Loss of heterozygosity (using B allele frequency) and find regions of CN alterations and LOH with or without Copy...number changes. Can anyone dire…

SNP affy SNP affy

updated 13.8 years ago • Guest User

I've created my gating set and I've loaded my gating template into R. When trying to gate I get the following error Error in (function (fs, pp\_res, gFunc, popAlias, channels, gFunc\_args...A1\_26a.fcs Error in matrix(ecol, length(include)) : data is too long I've used the same gating template for many of my other flow sets so I don't know why it would cause a problem now

opencyto gating

updated 8.5 years ago • justinyi10

<div class="preformatted">Hi Raj, In addition to aroma, there's also copy number estimation in crlmm and a hidden Markov model in VanillaICE that incorporates log R ratios and BAFs. Rob On Mar 17, 2012, at 7:00 AM, bioconductor-request@r-project.org wrote: > You can try aroma.affymetrix. Information specific to SNP 6.0 is located at > http://www.aroma-project.org/chipType…

SNP affy VanillaICE SNP affy VanillaICE

updated 13.8 years ago • Rob Scharpf

along a strange behaviour of biomaRt ensembl querys. I get different results when I use the filter "chromosome\_name" with values X chromosome and all autosomes or when I use values="\*" and then filter for the same chromosomes...This only happens with ggallus homolog attributes in the query.   <pre> ensembl.new <- useMart("ENSEMBL_MART_ENSEMBL",host="may2015.archive.ense…

biomart ensembl

updated 10.5 years ago • jmeisig

Hello, I would like to inquire about using DESeq2 package in order to compare different types of read data: 1. Would it be OK to use DESeq2 to compare read data between homologous genes __in different strains __of the same bacterial species? 2. In case I would like to analyze only a...compare different types of read data: 1. Would it be OK to use DESeq2 to compare read d…

deseq2

updated 7.9 years ago • yair.gatt

Dear community, I tried to download data by using "TCGAquery_recount2". But, I found the number of sample is different using different functions in TCGAbiolinks. Why does this happen? Thanks a lot! If I used TCGAquery_recount2...the number of samples is 601 (542 Tumor and 58 Normal) for TCGA-LAUD. While it is 594 (535 T and 59 N) for TCGA-LUAD if I used "GDCquery", "GDCdownload...TCGAquery_…

TCGAquery_recount2 TCGAbiolinks

updated 4.7 years ago • xiaofeiwang18266

Hi there, I have an RNA-seq dataset from a polyploid species (consisting of sets of similar chromosomes, which consequently, contain highly similar paralogs). I'd like to know whether I could compare expression between...sum of each replicate because it would underestimate the size of count differences to normalize by chromosome. For example, `rep_1` from the table below would be 100+130+450 (…

deseq2 edgeR normalization DGE

updated 6.2 years ago • grant.dejong

with the **plotAnnoPie** function of the ChiPseeker package. But unfortunately, for one single chart, the whole colour distribution is different....does anyone have an idea of how I can unify the plot-colors? I think that the...5 Downstream (<=300) 1.538462 4 Distal Intergenic 37.692308 My command for creating the pie-chart is: **plotAnnoPie(peakAnnoList_Peaks)** How can I creat…

ChiPseeker plotAnnoPie

updated 5.3 years ago • amafon95

<div class="preformatted">Hi, I wanted to plot the -log10 p-values of SNPs vs their chromosomal positions. I have an input file which looks like: Chr Ref Position p-value 1 rs100045 456789 0.00005 3 rs12345 23456...div class="preformatted">Hi, I wanted to plot the -log10 p-values of SNPs vs their chromosomal positions. I have an input file which looks like: Chr Ref Position p-value 1 r…

SNP SNP

updated 16.2 years ago • Paul Evans

of ChAMP results I was wondering if the frequency plot describe all the possible copy number alterations in all chromosomes and the sampleResult splitted in all samples dataset is the best kind of output to...extract the copy number data from CHAMP analysis. Thanks in advance. Best, Giovanni   &nbsp

champ

updated 7.5 years ago • Giovanni Calice

tilewidth=100, cut.last.tile.in.chrom=TRUE) }  \#\#\#\#\#\# test a 100Mb genome with 90 chromosomes (each chromosome is 1.1Mb) mySeqlengths90scaffolds <- makeSeqlengths( 100000000, 90 ) my\_var1\_90scaffolds..._var1\_90scaffolds, "binned\_var1") ) \#\# 2.1 seconds \#\#\#\#\#\# test a 100Mb genome with 900 chromosomes (each chromosome is 111.1kb) mySeqlengths90…

views iranges rle

updated 10.9 years ago • Janet Young

input data?? -- output of sessionInfo(): when i give more than 40 rows as input it shows blank chart -- Sent via the guest posting facility at bioconductor.org. </div

updated 13.2 years ago • Guest User

Enter the body of text here how to use R to convert chromosomal position information into SNP Code should be placed in three backticks as shown below ```r # include your problematic

SNPediaR

updated 2.3 years ago • wenbo

class="preformatted">Dear experts, Given the accession IDs such as these: How can I extract the "chromosome name", "start" and "end" position of each ID, with BioConductor. AB002292 AB002296 AB002298 AB002303 .. EF565109 K03493

updated 17.3 years ago • Gundala Viswanath

pre> Answer: Checking file validity Reading Channel Data Reading Raw Data Reading Template Data Reading Complement Data Reading Template FASTQ Error in .subset(x, j) : type 'closure' d'indice incorrect Could you

ioniser

updated 8.8 years ago • ferrato

list differentially expressed proteins with Entrez Gene ID. I would like to map these Gene ID to the chromosome location (start and stop) using R. Is there a package for this

annotation

updated 6.8 years ago • benjamin

for my Knock-out and Wilde Type samples. How should I go for displaying GOTerm on top EACH of Pie chart NODE? I can display GOID but I would like to have GOTerm. If anyone has done this before..plz let me know. below is code: if(require...counts[i,]) } if(missing(main)) main = "GO: Molecular Function : Mouse Embryo Fibroblast Pie Chart Plot" plot(curPlot,drawNode = drawing,main = mai…

GO graph GO graph

updated 21.3 years ago • SAURIN

Anyhow, I could just upload to UCSC the bed/bam/bedGraph/gff file containing ranges for multiple chromosomes. Then go to the browser-view to visualize any chromosome in a single window with my browser? On 2012-05-31, at 2:12 PM...gmail.com=""> wrote: >> Dear List, >> >> I wonder how to load RangedData for all chromosomes in a SINGLE tab in UCSC browse…

GO Cancer rtracklayer GO Cancer rtracklayer

updated 13.6 years ago • Yue Li

by Granges) of chr8 from BSgenome.Hsapiens.UCSC.hg19. I have the error of "No regions on given chromosomes". The following is the code: library("RSVSim") library("GenomicFeatures") library("BSgenome.Hsapiens.UCSC.hg19...i]] <- par[sel[i]] } return(par.list) } #getting chromosome 8 from genome. genome <- BSgenome.H…

software error

updated 5.7 years ago • mawen8898

I'd like to remove the genes on the X and Y chromosomes from my human RNA-seq data before doing differential analysis using DESeq2. I've looked through the _RNA-seq...I'd like to remove the genes on the X and Y chromosomes from my human RNA-seq data before doing differential analysis using DESeq2. I've looked through the _RNA-seq Workflow_

deseq2 rnaseq

updated 7.5 years ago • anpham

When I need to know the total sizes of chromosomes, I typically use the \`BSGenome\` package, which provides both metadata (like seqnames(BSgenome)) as well as raw sequence

bsgenome chromosome reference genome

updated 7.8 years ago • Nathan Sheffield

<div class="preformatted">Dear all, I have a data set consisted of 4 cell types with each cell type having 3 replicates. I find the unique signature genes of each cell types using decideTests (see following). I only want the top, say 20 signature probes that satisfy my thresholds. I tried to use "number=20" as for the "topTable" function with "decideTests", but it gave me the an error (se…

updated 14.6 years ago • Wendy Qiao

Hi, I am running into a pandoc-citeproc error when using BiocWorkflowTools' template Rmd file for an F1000 article. I updated both pandoc and pandoc-citeproc using brew, thinking that it could help with...worry about the citations later. Best, Leo   <pre> > rmarkdown::draft("MyArticle.Rmd", template="f1000_article", package="BiocWorkflowTools") > rmarkdown::ren…

BiocWorkflowTools rmarkdown

updated 8.6 years ago • Leonardo Collado Torres

my nanopore data <pre> Checking file validity Reading Channel Data Reading Raw Data Reading Template Data Reading Complement Data Reading Template FASTQ Error in strsplit(strings, "\n") : non-character argument</pre> This

ioniser software error bioconductor

updated 9.2 years ago • mv340788

<div class="preformatted">Dear Bioconductors, I have genotyped 8 samples from Affy6.0 platform using crlmm algorithm from Oligo and I am facing difficulties in interpretation. I am trying to match the gender from the phenodata with the SNP calls from crlmm on X and Y chromosomes. I would appreciate any comments and help. Given a SNP has A and B allele, is it that A is always a major allele…

SNP oligo crlmm SNP oligo crlmm

updated 15.7 years ago • jeremy wilson

nbsp; I'm trying to work out a function or find a package that lets me normalize omics data to cell number.  So after counting cells for a certain condition and running the omics experiment, I would use the mean cell count...this would be? Perhaps there's already a package available that allows me to specify the cell count number?  Thank you

normalization normalize cell

updated 7.6 years ago • bhgyu

n) colorpanel(n, "blue", "white", "brown") > > you can fit in every color from the R color chart, which you can find here: > http://research.stowers-institute.org/efg/R/Color/Chart/ > > in the heatmap-command you set

updated 16.8 years ago • Amy Johnson

I am trying to run the TCGAvisualize\_EAbarplot function, but instead of producing the expected charts it produced nothing, specifically it runs the function, then after the last step says null device. Any ideas why it didn

tcga

updated 8.2 years ago • pgreylin

I get this output: Checking file validity Reading Channel Data Reading Raw Data Reading Template Data Reading Complement Data Reading Template FASTQ Reading Complement FASTQ Error in strsplit(strings, "\\n") : non

IONiseR

updated 8.8 years ago • artemd

Error in easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = "auto", : The number of conditions: 0 did not correspond to the number of samples: 1 In addition: Warning messages: 1: In easyRNASeq(filesDirectory...getwd(), organism = "Hsapiens", chr.sizes = "auto", : You enforce UCSC chromosome conventions, however the provided chromosome size list is not compliant. Correct…

Annotation Organism easyRNASeq DESeq2 Annotation Organism easyRNASeq DESeq2

updated 12.3 years ago • Aki Hoji

I would like to plot aligned reads from a `` bam `` file over a specific region. Everything works fine with the following command: <pre> alTrack <- AlignmentsTrack(my.bam.file, isPaired=TRUE) snp.pos <- 308632 plotTracks(alTrack, chromosome="chr1", from=snp.pos-200, to=snp.pos+100)</pre> But shortening the region (by increasing `` from ``) results in an error: <…

gviz plottracks alignmentstrack

updated 8.9 years ago • TimothéeFlutre

Hi All, I have been using the annotatr package to annotate differentially methylated regions (DMRs) and differentially methylation CpGs/positions (DMPs) and create bar charts based on these results. However, it seems to be duplicating some of the entries. I realize some areas may map to multiple locations in the genome, but I would like to eliminate duplicates if possible. For example, I have …

annotatr AnnotationHub

updated 23 months ago • hayleyw

analyze the data, and normalizing it with the preprocessFunnorm function. All the cases have a copy number variation (CNV) encompassing multiple genes. 1) Should I expect to see difference in methylation for the probes contained...within the CNV (due to the different copy number) or would the difference in probe intensity between cases and controls be normalised? 2) If I the observed difference…

CNV minfi preprocessing dna methylation

updated 8.8 years ago • Thomas

crlmm in the BioC 2.7 release branch was updated. This update addresses the NA's reported for copy number at nonpolymorphic markers on chromosome X. Thanks- Rob </div

crlmm crlmm

updated 15.1 years ago • Rob Scharpf

help/bioconductor-cloud-ami/#multiple if you click the Start MPI Cluster<https: bioc-cloudformation-templates="" cloudformation="" cluster.json="" console.aws.amazon.com="" east-1#cstack="sn~StartBioCMPICluster|turl~https://s3.amazonaws.com...an error stating that the JSON is invalid in the file https://s3.amazonaws.com/bioc-cloudformation-templates/cluster.json Thanks! Jason Miller JiWire…

updated 12.2 years ago • Jason Miller

<div class="preformatted">I just stumbled upon some oddities with rtracklayer and data generated from the NCBI/Ensembl annotation of the Drosophila genome. It seems like bigwig saved with the official NCBI/Ensembl/flybase mitochorion chromosome name dmel_mitochondrion_genome breaks the importation of a previously saved files (which does not break when loaded in other tools like the Broad IG…

Coverage Annotation rtracklayer Coverage Annotation rtracklayer

updated 11.6 years ago • Marco Blanchette

vega_mart_47 Vega 5 compara_mart_homology_47 Compara homology 6 compara_mart_multiple_ga_47 Compara multiple alignments 7 compara_mart_pairwise_ga_47 Compara pairwise...vega_mart_46 Vega 12 compara_mart_homology_46 Compara homology 13 compara_mart_multiple_ga_46 Compara multiple alignments 14 compara_mart_pairwise_ga_46 …

cdf probe affy graph limma biomaRt cdf probe affy graph limma biomaRt

updated 16.9 years ago • Jesper Ryge

disease type VI)" > get('202100_at', hgu133aGENENAME) [1] "v-ral simian leukemia viral oncogene homolog B (ras related" [2] " GTP binding protein)" > get('202990_at', hgu133aGENENAME)[1] [1] "phosphorylase, glycogen" > get('202990_at...type VI)" > get('202100_at', hgu133aGENENAME)[1] [1] "v-ral simian leukemia viral oncogene homolog B (ras related" > get('2…

Leukemia Leukemia

updated 19.3 years ago • Shi, Tao

To be specific, in the microarray format. Is there a function also the represent the data in pie chart format? Thank you for the help <span style="line-height:1.6">Sowmya </span> &nbsp

data representation in graphical forms

updated 10.8 years ago • sow19872003

I’m experimenting with the ability of fry/mroast functions to include gene weights. I have two use cases:   __1) Comparing the result of a previous experiment in mouse, with a current experiment in human: __Basically I want to see if a previous observed response in mouse is observed in a similar human experiment. I can use Ensembl homologs to match results from the mouse data to the hu…

limma mroast fry

updated 7.3 years ago • maltethodberg

of functional profiles for genes and gene clusters cn.farms Factor Analysis for copy number estimation ENVISIONQuery Retrieval from the ENVISION bioinformatics data portal into R ExiMiR R functions for...data class for gated flow cytometry data gaia An R package for genomic analysis of significant chromosomal aberrations genefu Relevant Functions for Gene Expression Analysis, Es…

SNP Sequencing miRNA Microarray Annotation Normalization Pathways Preprocessing Network

updated 14.7 years ago • Dan Tenenbaum

an RNAseq experiment. What is not clear to me is on what basis to chose `m1` which is the "expected number of prognostic genes". Is it the number of significant genes I identified in my own dataset? For the example below, the power...estimation by read count and dispersion distribution est_power_distribution( n = 20, # Number of samples in each group m = 12, # Total num…

RnaSeqSampleSize

updated 4.5 years ago • Matthias Munz

a list of genes (Affy ID), and an expression value >for each gene. >1. how can I draw a map of chromosomes, on which the genes >are marked? >2. is it possible to color-code the genes on this map? > >Is there any package

Cancer geneplotter Cancer geneplotter

updated 20.9 years ago • John Zhang

to load an FCS file containing multiple data segments, and am trying to automate the process but the number of datasets varies - I would like to be able to automatically get the number of data segments to then use a loop to store...them all. There seems to be some built-in function for quickly checking the number of segments, as if I use ```read.FCS``` without specifying a dataset, it instantly r…

flowCore

updated 4.8 years ago • mark.holmes

I was running this function CNA <- function(genomdat, chrom, maploc, data.type=c("logratio","binary"), sampleid=NULL, presorted=FALSE) { if (is.data.frame(genomdat)) genomdat <- as.matrix(genomdat) if (!is.numeric(genomdat)) stop("genomdat must be numeric") if (!is.numeric(maploc)) stop("maploc must be numeric") data.type &lt…

DNAcopy

updated 5.1 years ago • El

In the current `` GenomicFeatures `` package (Bioc 3.2), `` makeTxDbPackage `` uses the "Data source" metadata to set the Provider and ProviderVersion fields of the txdb template, even though these should sometimes (always?) be different. Could this be fixed for Bioc 3.3? Moreover, it would help if...uses the "Data source" metadata to set the Provider and ProviderVersion fields of the txdb templ…

genomicfeatures txdb maketxdbfromgff metadata

updated 9.7 years ago • TimothéeFlutre

validity</pre> <pre> Reading Channel Data</pre> <pre> Reading Raw Data</pre> <pre> Reading Template Data</pre> <pre> Reading Complement Data</pre> <pre> Reading Template FASTQ</pre> <pre> Error in strsplit(strings, "\n") : non-character

R sequencing preprocessing bioconductor

updated 10.0 years ago • mariandhore

http://prs.ism.ac.jp/bioc/2.7/bioc/html/DNAcopy.html) in order to plot my agilent CGHarrays (mouse):(chromosome in X axis and logR in Y axis) I have 2 questions about this package: I have done the data segmentation using the segment...one plot ( "w" option) example : plot(segment.smoothed.CNA.object, plot.type = "w") question 1: the chromosomes alternate in different colours and are sorted in th…

probe DNAcopy probe DNAcopy

updated 14.6 years ago • nac

build a data package. I can fairly easily make an environment that contains (for this example) chromosome location (in BP) or chromosome number mapped to my geneIDs (from local data sources). How can I use these simple environment

Annotation geneplotter Annotation geneplotter

updated 22.2 years ago • Sean Davis

Dear All, I am currently using the Basic4Cseq package to analyze my 4C data.. the analysis pipeline seems fine.. I used two "4-based" cutters to generate my library and my goal to generate a wig file to find trans interactions and further downstream analysis.. the following is the pipeline I used ## Bam to Wig using Basic4Cseq library(Basic4Cseq) library(BSgenome.Hsapiens.U…

GenomicInteractions Basic4Cseq DNASeq GenomicFiles

updated 4.5 years ago • koushik

found out that some reads reported in Rsubread's SAM output have their end positions outside of the chromosome ranges. If those reads are removed from the SAM file then the import into Rsamtools works just fine. Below is a reproducible...this problem. I could think of several solutions to fix this, e.g. not reporting reads outside of chromosome ranges or updating their length in the CIAGR string…

PROcess Rsamtools Rsubread TCC PROcess Rsamtools Rsubread TCC

updated 13.9 years ago • Thomas Girke

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

GO biomaRt GO biomaRt

updated 14.5 years ago • james perkins