Bioconductor Forum

div class="preformatted">hi all, i would like to perform hyperGTest using the chromosome position (stored usually in pkgMAP environment). how could it be possible? thank you for your help! greetings d -- Dario

updated 19.0 years ago • Dario Greco

div class="preformatted">Dear all, I have data of the following format Genbank Acc ID Chromosome Start Stop Statistic NM_003146 11 313333 316345 3.4 AK023401 11 303313 310315 -3.1 AF086195 10 613323 716385...412341 4.5 ... ... ... where Start and Stop indicate the start and stop position in the Chromosome mention…

updated 22.4 years ago • Adaikalavan Ramasamy

segmentation using the segment () function and now I want to plot my data using plot(). I know that chromosome 15 is duplicated in my samples. -With this configuration plot type=w ( plot all the genome) plot(segData, plot.type...w") , the chromosomes alternate in different colours and the duplicated chromosomes are not in the right place ( it says chro7 is duplicated...and I know it should be 1…

DNAcopy DNAcopy

updated 14.6 years ago • nac

segmentation using the segment () function and now I want to plot my data using plot(). I know that chromosome 15 is duplicated in my samples. -With this configuration plot type=w ( plot all the genome) plot(segData, plot.type...w") , the chromosomes alternate in different colours and the duplicated chromosomes are not in the right place ( it says chro7 is duplicated...and I know it should be 1…

DNAcopy DNAcopy

updated 14.6 years ago • nac

clusterProfiler to do gene enrichment for a non-model species. After I annotated my gene sets to K numbers, I noticed different genes might be annotated as the same K number. Should I get the unique K number set to do gene enrichment...or use all K number to do functional enrichment? Will this influence my result? And I also need to get the K number for my whole genome to make...it as the back…

clusterProfiler

updated 5.0 years ago • XM

version 1.4 and SNPchip 1.4. I am new to high throughput SNP analysis. My goal is to perform copy number / LOH analysis on tumor tissue samples processed with Affymetrix 100K SNP chips. Question : 1. My understanding is that...to work on in SNPchip. How do I use oligo to generate an oligoSNPset class object? (genotypes + copy number). In a related 2nd question, I need to merge the oligoSNPset c…

SNP Cancer graph oligo SNPchip oligoClasses VanillaICE crlmm SNP Cancer graph oligo

updated 16.7 years ago • Min-Han Tan

where we put a transgene in mice cells, my gene of interest (that transgene) is on an "artificial" chromosome which contains only this gene. I'm trying desesperately to isolate that chromosome from the data, using R package

rnaseq r cummerbund

updated 9.1 years ago • guillaume.dachy

an issue while opening a FlowJo (version 10.0.8) Workspace file for using it as a gating template. The problems are: 1) FlowJo cannot save the workspace as .xml format file, which seems to be the only format that openWorkspace...function takes while opening the gating template; My flowJo version only saves the workspace as .wspt or .xls files, and I even converted my gating template to .xml…

opencyto gating opencyto flowcore flowworkspace

updated 9.7 years ago • anara92

bundled together into an archive then `` parseWorkspace ``seems to work.  I then generated a template file using the `` templateGen ``function. After modifying the gating method column in the csv template file I try to import...the template back using the `` gatingTemplate `` function, whereby I get an Error in .validity_check_alias(this_row[, alias]) : …

opencyto

updated 8.2 years ago • biomiha

div class="preformatted">Not sure if this needs using Bioconductor. To get the chromosome position(in bp, Build36) for a BAC clone, eg 'RP11-189K9', I was following this post: http://article.gmane.org/gmane.science.biology.informatics.conductor

GO BAC GO BAC

updated 17.1 years ago • Al Tango

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 TMX2.    Is there a programmatic way to remove the incorrect conversion? library...mgi\_symbol"), filters = "mgi\_symbol", values = genes ,mart = mouse, attributesL = c("hgnc\_symbol","chromosome\_name", "start\_position"), martL = human, uniq…

biomart gene symbol

updated 10.5 years ago • chang02_23

<div class="preformatted">Hi, The new Ensembl marts for release 54 are now live on www.ensembl.org. The following improvements and modifications have been made: Mart Builds (all species) Ensembl mart 54: * New assembly for Zebrafish (Zv8) plus corrected assembly names for various other species. * Corrected Zebrafish attribute Agilent g2519f internal naming error reported by BioCo…

Coverage zebrafish Coverage zebrafish

updated 16.7 years ago • Rhoda Kinsella

Hello all,   Is there a possible way to index bam files for large chromosomes(like wheat) using Rsamtools? Like in case of samtools using linux, .CSI (coordinate sorted index) is possible...whereby .bam files for large chromosomes can be indexed. However, the .CSI index generated using samtools (through linux) is not compatible with MEDIPS

Rsamtools QSEA MEDIPS

updated 7.2 years ago • saripalligautam86

Hello All,   Is there a possible way to index bam files for large chromosomes(like wheat) using Rsamtools? Like in case of samtools using linux, .CSI (coordinate sorted index) is possible...whereby .bam files for large chromosomes can be indexed. However, the .CSI index generated using samtools (through linux) is not compatible with MEDIPS

csi index Rsamtools wheat

updated 7.2 years ago • saripalligautam86

Tracks (regs and rl14regionsR) in the same plot using Gviz along with an IdeogramTrack for chromosome 14 under hg38 with the following code: gen<-"hg38" chr="chr14" atrack<-AnnotationTrack(regs, name= paste0("All expressed...transcriptAnnotation = "symbol", background.title = "brown") gtrack <- GenomeAxisTrack(chromosome = …

gviz genomicranges

updated 8.4 years ago • rtonalli

between two set of GRanges objects, and I want to split theses regions into sub regions by order of chromosome. Intuitively, take all genomic regions from each chromosome and iterate over. Any hint to do this in R ? Thanks a lot

granges split r

updated 9.9 years ago • Jurat Shahidin

1.6">Hi,</span> Somatic signatures package uses RSS and unexplained variance to assess the best number of signatures. In Alexandrov et al paper (Cell Reports 3, 246-259) they used cosine similarity and Frobenius reconstruction...error to determine the number of signatures. Did any one compare the two ways and find difference in determination of number of signatures? Thank

somaticsignatures

updated 10.4 years ago • Asma rabe

gives expected result, all 6 ranges intersect(gr1,gr2) # includes ranges from the missing gr2 chromosomes setdiff(gr1,gr2) # includes 3 copies of the ranges from the missing gr2 chromosomes sessionInfo() R version 2.11.0

updated 15.5 years ago • Cei Abreu-Goodger

use default substitution matrix /usr/include/c++/8/backward/auto_ptr.h:198: std::auto_ptr< <template-parameter-1-1> >::element_type* std::auto_ptr< <template-parameter-1-1> >::operator->() const [with _Tp = clustalw::FileParser...std::auto_ptr< <template-parameter-1-1> >::element_type = clustalw::FileParser]: Assertion '_M_…

msa

updated 2.9 years ago • systems

which needs generation of missende variants an subsequent conversion of RefSeq data to its referring chromosomal position. I am currently retrieving the RefSeq sequence in R using biomaRt and create a .txt file that I am then

RefSeq Chromosome Mutalyzer

updated 5.7 years ago • heiko_kin

div class="preformatted">Hi all, I am running into problems when I want to remove probes targeting chromosome Y. I can reproduce this behavior with the data from the beadarrayExampleData package: library(beadarray) library...No match" | qual == "Bad" | is.na(qual) exampleSummaryData_filt = exampleSummaryData[!rem] ## get chromosome location for remaining probes ids = as.character(featureNam…

probe probe

updated 12.8 years ago • Kemal Akat

look at the documentation? I have: whether a given probe id can be mapped to a single or multiple chromosomal locations. + and - signs are used to indicate the the strand of the chromosome. The names give the chromosome number...of concern. NA is assigned to probe identifiers that can not be mapped to any chromosomal location data at this time. Mappings are obtaine…

probe probe

updated 22.2 years ago • rgentleman

Hello, I've used the Gviz User Guide to create a figure displaying a chromosome ideogram, the coordinate axis, a model of a single gene, and data points indicating the number of variants reported...coords <- append(numvars.sort$V2, 117308178) itrack <- IdeogramTrack(genome="hg19", chromosome="chr7") gtrack <- GenomeAxisTrack(littleTicks=TRUE) …

gviz r

updated 10.8 years ago • melissalee0

is 215210_s_at On the other hand, 217216_x_at is "mismatch repair gene MLH3, mutL (E.coli) homolog 3; mutL homolog 3". hgu133plus2GENENAME and hgu133plus2GENENAME are both incorrect. I didn't test others. Please let

Annotation affy Annotation affy

updated 20.8 years ago • Kevin Dawson

I would like to calculate some sliding statistics across chromosomes. What are the preferred methods used for such purposes? Thanks

sliding statistics

updated 6.9 years ago • joyce

preformatted">Hi there, I'm preparing a tutorial, therefore I sliced two RNASeq bam files from chromosome one, in order to reduce the file size. However, when I count the reads as it follows I have an error. thanks, Francesco...GL000241.1", : (list) object cannot be coerced to type 'integer' I also tried selecting the chromosome with chr.sel=c("1") or chr.sel=c("chr1") but in both cases I …

RNASeq Alignment BSgenome BSgenome RNASeq Alignment BSgenome BSgenome

updated 13.9 years ago • Lescai, Francesco

Hello, I want to find gene on chromosome 6 using __TxDb.Hsapiens.UCSC.hg19.knownGene__ package, and I use two different methods, but the genes found...Hello, I want to find gene on chromosome 6 using __TxDb.Hsapiens.UCSC.hg19.knownGene__ package, and I use two different methods, but the genes found were not identical. Following was the code: <span style="line-height:1.6">load the library&…

txdb.hsapiens.ucsc.hg19.knowngene txdb

updated 9.4 years ago • li lilingdu

to understand how the index from the synteny analysis in the DECIPHER package can be translated into chromosomes. I basically used what is in the official website: <pre> # load the DECIPHER library in R library(DECIPHER) # specify...2] 1962640 CTAACTTGACACCTTTCCCTTG...TCATTCCTCTTCCCACACACAC 1.Genome3 </pre> Checking the chromosome of the first part of the sequence of Genome3…

decipher

updated 8.0 years ago • Vinicius Henrique da Silva

preformatted">Hi all, I have a list of mapped sequence reads to hg18 for that I have the exact chromosomal location on NCBI build 36. Cluster ID Strand Chromosome Cluster_Begin Cluster_End slc754_chr2 + chr2 74295624...subscript out of bounds" error. I tried splitting the localization infos into separate vectors, i.e. chromosome &lt…

biomaRt ASSIGN biomaRt ASSIGN

updated 15.2 years ago • Kemal Akat

rss115 at case.edu -- output of sessionInfo(): Hello, I have generated piechart of differentially expressed proteins(dataset-x) using GO.CC in GeneAnswers package.Is it possible to get the list of proteins present in a particular cellular compartment for.eg-genes present in cytoplasm, genes present in intracellular component? Looking forward for suggestions Thanks in advance, Roopa -- Sen…

GO GeneAnswers GO GeneAnswers

updated 14.2 years ago • Guest User

white", cex=5) > mir\_track  AnnotationTrack 'miR-150' | genome: GRCh37 | active chromosome: chr19 | annotation features: 1   \#annotation for promoter promoter\_track <- AnnotationTrack(promoter\_grange...stacking="squish") \#), rot.title=0) AnnotationTrack 'promoter' | genome: GRCh37 | active chromosome: chr19 | annotation features: 1 &…

gviz

updated 9.4 years ago • just

to know how can i download the conservation track for several genomic ranges belonging to different chromosome sequences as the example below seems only to retrieve this information for 1 of the chromosomes, (the first one

updated 16.5 years ago • Robert Castelo

I finally made it to the 24chr DNAcopy multiplot but as my chromosomes are already named chr1 ... I get plot titles like 'Chromosome chr1' which is not nice and too long to see the actual chr...number. Ideally, I would like to not print 'Chromosome' Is it possible to substitute the plot titles with a vector of names. my current...command is:   \# one plot per chromosome in mosaic &am…

DNAcopy

updated 8.2 years ago • Stephane Plaisance | VIB |

recombination generates novel combinations of genetic variation via reciprocal exchange between homologous chromosomes. To better understand this process we are generating genome-wide recombination frequency maps

Genetics Arabidopsis thaliana PROcess Genetics Arabidopsis thaliana PROcess

updated 14.1 years ago • Krys Kelly

field of your seed file is probably a bad idea anyway. This field is typically expected to list the chromosomes or "top-level sequences" so it will always have a small number of entries (i.e. < 100). Things like contigs or scaffolds...gt;> forgeBSgenomeDataPkg() to break? >> >> The answer is no. Once I reach a certain number of fasta files, adding one &am…

GO Cancer BSgenome BSgenome genomes GO Cancer BSgenome BSgenome genomes

updated 12.8 years ago • Hervé Pagès

chr1", "chr2"), ranges = IRanges(start = 1:2, end = 4:5)) ``` I want to change the chromosome names all to "chrX" ``` > seqnames(gr) <- "chrX" Error in .normalize_seqnames_replacement_value(value, x) : levels of supplied

genomicrang GenomicRanges

updated 4.2 years ago • changxu.fan

div class="preformatted">Dear all, I'm trying to use biomaRt to map the chromosome location to gene ID,( I got chromosome number, start position and stop position, and it's for human) May I ask the syntax

biomaRt biomaRt

updated 14.6 years ago • Yan Jiao

From this link [remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline ][1], I have learned that depending on context, it is perfectly valid to...remove X and Y chromosomal genes in RNA-seq data before doing differential expression analysis. However I only have access to the count...and not the **bam** files of the RNA seq data I am analysing. Is it advisable to do the X and Y chro…

deseq2

updated 6.7 years ago • charlesgwellem

Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|1|0.42|0.75|8|1603| 7 maker-Contig1111-pred_gff_snap_masked-gene...Contig6333-snap-gene-0.51-mRNA-1 transcript Name:"Similar to NDE1 Nuclear distribution protein nudE homolog 1 (Gallus gallus)" offset:46 AED:0.16 eAED:0.16 QI:46|1|1|…

RNASeq edgeR a4 RNASeq edgeR a4

updated 12.0 years ago • Guest User

Hello! My question is about reads that don't align to the genome yet are long and have very good Phred scores. Currently, my workflow is FastQC > Cutadapt > Trimmomatic > RNA-STAR > HTSeq-count > edgeR (RUVSeq) I use gencode genomes with Ensembl IDs and even with the cleanest isolation of cells and excellent library production I still get about 80% alignment to…

rnaseq alignment

updated 9.2 years ago • Matthew Thornton

div class="preformatted">The GenomeSearching vignette promises that injecting known SNPs into chromosome sequences is coming soon. I am sorry to be pesky, but may I ask just how soon? I'd love to use this feature now. Best, - Paul

updated 16.9 years ago • Paul Shannon

I'm working with a species that does not have sex chromosomes. The only part of the workflow in which I see I can note this is while building the GRM – by setting the option autosome.only...looked through R documentation for assoctestMM and don't see a way to specify that there are no sex chromosomes in this dataset. How can I do this? Thanks for your time. Here are relevant lines prior to …

GENESIS assoctestmm GWAS

updated 7.4 years ago • naglemi

Having successfully run analyzeChr() on chromosomes up through 22 and X (but not higher-numbered chromosomes, see <https://support.bioconductor.org/p/62551/>), I ran mergeResults...Having successfully run analyzeChr() on chromosomes up through 22 and X (but not higher-numbered chromosomes, see <https://support.bioconductor.org/p/62551/>), I ran mergeResults() to move forward with anal…

derfinder

updated 11.2 years ago • jessica.hekman

class="preformatted">Hi All i have a object gp = c(1,2,3,4,21,22,23,24,38,39) and i want to count number of groups containing consecutive numbers as ans should be three as group1 (1,2,3,4), group2 (21,22,23,24) and group3 contains

updated 15.4 years ago • ALok

When testing more gene sets with `` mroast ``, should number of rotations be increased to maintain the accuracy of p values? If I use x number of rotations for testing 1 gene set, should...When testing more gene sets with `` mroast ``, should number of rotations be increased to maintain the accuracy of p values? If I use x number of rotations for testing 1 gene set, should I use perhaps 10x numbe…

limma mroast

updated 7.4 years ago • siajunren

Hello, I'm looking for some R package or even software to make methylation profile of chromosomes. I found two very nice packages for R: ChromHeatMap (plots made by this are what I'm looking for) quantsmooth Unfortunetaly

R heatmap

updated 9.4 years ago • Adam

Hello everyone, does anyone know if and how I can remove border events in all channels without specifying each channel in the template? Also, I would like to have a time gate, is this possible? I know i can do both with flowcore, but I also like the idea of a readable...know if and how I can remove border events in all channels without specifying each channel in the template? Also, I would lik…

opencyto gating flowcore flow cytometry

updated 9.7 years ago • Ulrik Stervbo

I have single ended 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 --stran…

deseq deseq2 edger tophat bowtie

updated 10.5 years ago • ysdel

epigenetic modifications, etc.) associated with a list of retroviruses (whose description and chromosomal position are stored in a local database) within R. After a quick literature review (AnnotationForge vignettes...that custom chip packages can only be built by mapping probeset identifiers with gene accession numbers. Since we are not looking at conventional genes, we cannot map our c…

annotation package custom microarray

updated 10.9 years ago • becker.jeremie

have the mouse homologue. If I am running this script I do not know which probe is homologue to >homolog = getHomolog( id = c("1939_at","2000_at"), to.array = "affy_mouse430_2 ", from.array ="affy_hg_u95av2", from.mart = human, to.mart...mouse ) >show(homolog) V1 1 1427739_a_at 2 1426538_a_at 3 1428830_at 4 1421205_at I also tried with getBM but no su…

probe affy probe affy

updated 19.1 years ago • marco fabbri

total count. GoTools provides the other methods for this purpose: TGENES: for each endnode, return number of children for this node / number of oligo (genes) in the group of oligos you provide: ontoCompare(affylist,probeType...L2: 64/90 = 0.71 L3: 52/70 = 0.74 TIDS: for each endnode, return number of children of this node / total number of GO ids describing the group of oligos you provide. o…

GO hgu133a probe PROcess goTools oligo GO hgu133a probe PROcess goTools oligo

updated 18.9 years ago • Paquet, Agnes

Hi all, I recently started analysing a mouse RNA-seq dataset, where I had the following data: * 6 control samples, all of them contaminated with a human cell line * 6 KD samples with no contamination After seeing the "experimental setup" my first thought was to just trash it, take a deep breath, and tell the collaborators to redo the experiments/sequencing as the contamination and the cont…

rna-seq salmon tximport limma

updated 8.7 years ago • Endre Sebestyen

<div class="preformatted">Hi All! I have 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, which is capable...I have a list of genes (Affy ID), and an expression value for each gene. 1. how can I draw a map of chromosomes, on w…

updated 20.9 years ago • Dr Gyorffy Balazs

for Codelink platform these days and found this problem exist, but only in the human arrays. No chromosome locations are found. The annotations created for both mouse and rat arrays have the corresponding chromosome...0.99-7" "1.10.0" I have and old build from Mon Jan 16 06:53:47 2006 that has the corresponding chromosome location but I don't have information about sessionInfo(), only that it…

Annotation GO annotate affy AnnBuilder codelink Annotation GO annotate affy AnnBuilder

updated 19.7 years ago • Diego Diez

R. If I search the CpG's name on UCSC Genome Browser on Human (GRCh37/hg19), I can get the name of Chromosome and the genomic position( Example cg00000029 : chromosome ch16; genomic position 53,468,112). But I cannot search

GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData

updated 20 months ago • Yveto

I have some bam files with chromosome names like "1" instead of "chr1". I run into problems when I want to plot data from ensembl along with coverage data...I have some bam files with chromosome names like "1" instead of "chr1". I run into problems when I want to plot data from ensembl along with coverage data from...I would like to modify the function that reads data from the bam file somehow so…

gviz

updated 9.0 years ago • stianlagstad

time to time: <code>Detecting candidate regions with coefficient larger than 0.05 in magnitude.<br/> ...Chromosome chr1: Smoothed (0.89 min). 335 regions scored (1.64 min). <br/> ...Chromosome chr10: Smoothed (0.74 min). 117 regions scored...0.38 min). <br/> ...Chromosome chr11: Smoothed (0.65 min). 119 regions scored (0.34 min). <br/> …

dmrseq

updated 7.2 years ago • kuckunniwid

samples=read.csv("GW_S3_SampleSheet.csv") inputExp <- ChIPQC(samples,annotation = "hg19",chromosomes=1) ``` When I chose one chromosome to investigate, everything went well. However, when the number of chromosomes increased...error appeared (only in BiocParallel ). ```r inputExp <- ChIPQC(samples,annotation = "hg19",chromosomes=c(1,2)) ##Error: BiocParallel errors ##0…

BiocParallel ChIPQC

updated 15 months ago • Young Boqin

like the title says, I am looking for a concise and high-performance way to extract only the chromosome name and read start position from a BAM file. It can be easily done from outside R like this: <pre> samtools view my.bam

bam rsamtools samtools genomicalignments

updated 9.7 years ago • Vang Le

are different from what we expect (UCSC standards), as they have an additional .fa extension levels(chromosome(aln)) ## faster than a table on the same content: table(chromosome(aln)) ## they are different from what biomaRt will return...are in the genomicAnnotation slot gAnnot <- genomicAnnotation(obj) ## shall we subset to the chromosome we're interested in ## there are only 1181 NT co…

RNASeq Annotation Organism biomaRt easyRNASeq RNASeq Annotation Organism biomaRt

updated 13.8 years ago • delhomme@embl.de