Bioconductor Forum

implementation of the read.dcf() function. Having so many entries in the 'seqnames' 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...to a call to read.dcf() made in the > forgeBSgenomeDataPkg() that is used to read the seed file. I came to the > realization that there is an upper limit to t…

GO Cancer BSgenome BSgenome genomes GO Cancer BSgenome BSgenome genomes

updated 12.8 years ago • Hervé Pagès

<div class="preformatted">Hi John, I am having trouble reproducing this. Can you please send me your "ilmn_cust_raw.txt" file along with the sessionInfo() when you built your package? Marc John Lande wrote: > dear All, > > I am trying to build an annotation package with annotationDbi. I followed > the instruction to build the package, with this script: &…

Annotation affy AnnotationDbi Annotation affy AnnotationDbi

updated 15.9 years ago • Marc Carlson

not publicly available) I've looked through the vignette and I'm stuck on how to construct the seed object. I know how to generate a BSgenome object using forgeBSgenomeDataPkgFromNCBI(), but I'm stuck on how to construct

BSgenome BSgenomeForge

updated 3 months ago • mat149

but after running CATALYST::cluster(sce, features = NULL, xdim = 10, ydim = 10, maxK = 20, seed = 1234) I only have 11 markers left.... DataFrame with 11 rows and 4 columns channel_name marker_name marker_class used_for_clustering

CATALYST SingleCellExperiment

updated 5.0 years ago • achaillon

mytrain <- pamr.train(mydata) mycv <- pamr.cv(mytrain,mydata) But if you change the seed, it doesn't: set.seed(1123) x <- matrix(rnorm(1000*20),ncol=20) y <- sample(c(1:4),size=20,replace=TRUE) mydata <- list(x=x,y=y) mytrain

GO pamr GO pamr

updated 21.4 years ago • Dick Beyer

<div class="preformatted"> I am in just the same problem as yours now. I think there are two key steps in the RMA that depend on the set of chips in a run. One is quantile normalization step, and the other is median polish summarization step. The target value of each quantile of probe intensity is the geometrical mean calculated from the same qunatiles across the entire chip set in the run…

Normalization probe PROcess Normalization probe PROcess

updated 20.6 years ago • t-kawai@hhc.eisai.co.jp

gt; library(oligo) > cels = list.celfiles() > raw = read.celfiles(cels) > pp0 = rma(raw, target='core') > pp1 = rma(raw, target='probeset') > > to obtain your preprocessed data through oligo. > > The annotation package...to create your package: > > ## code to build HTA annot pkg > library(pdInfoBuilder) > seed &am…

Annotation oligo pdInfoBuilder Annotation oligo pdInfoBuilder

updated 11.7 years ago • Elena Serrano

Ca\_chr1.fa” and “Ca\_chr2.fa” located in  /Users/Cicer/seqs/   Then I have created a seed file ("cicer") which it is also included into that folder. The seed file looks like this :  Package: BSgenome.Carietinum.NCBI.ca1

bsgenome bsgenome forge

updated 8.5 years ago • jodiera

errors when building the library for a 12plex yeast genome expression array.... makePdInfoPackage(seed, destDir = "/Library/Frameworks/R.framework/Versions/2.15/Resources/library/") ====================================================================== ========== Building annotation package for Nimblegen

Annotation Yeast oligo pdInfoBuilder Annotation Yeast oligo pdInfoBuilder

updated 13.6 years ago • Simon Melov

pmFeatures"]], tiledRegionPmFeatureSchema[["col2type"]], !quiet) 2: makePdInfoPackage(seed, destDir = "/Users/kturner/Desktop/") 1: makePdInfoPackage(seed, destDir = "/Users/kturner/Desktop/") Many thanks in advance for any

Annotation pdInfoBuilder Annotation pdInfoBuilder

updated 14.9 years ago • Kate Turner

negative extents to matrix OR When i am building annotation package: > makePdInfoPackage(seed, destDir = ".") ====================================================================== ========== Building annotation package for Nimblegen Expression Array NDF: 2006-08-18_TI4932_60mer.ndf XYS: 50186202_532.xys...quiet) : Control probe possibly identified as Experimental I know, I Know, this …

Annotation probe Annotation probe

updated 15.5 years ago • Marcelo Brandão

nPerm = 1000, exponent = 1, minGSSize = 10, pvalueCutoff = 1, pAdjustMethod = "BH", verbose = TRUE, seed = FALSE, by = "DOSE") preparing geneSet collections... calculating observed enrichment scores... calculating permutation scores

clusterprofiler gseGO plotGOgraph() topGO

updated 8.9 years ago • cjsifuen

nbsp;                          seed=1422976420,verbose=FALSE) i know the R the least,,,i read the manual but really i could not find any clue. i really need your

software error network

updated 10.2 years ago • Angel

nbsp;  TERM2NAME = NA,      verbose = TRUE,      seed = FALSE,      by = "fgsea") " \#\# <pre> preparing geneSet collections... --> Expected input gene ID: 94094,223650,17926,12831

GSEA clusterProfiler

updated 8.1 years ago • giuseppe0525

data with edgeR and implementing glmTreat to find significantly DE genes. I am comparing dry soybean seeds to "dead" and "alive" soybean seeds after 24 h imbibition. I noticed in the documentation that glmTreat uses unshrunk log...y <- calcNormFactors(y) # define model design matrix. since all comparisons are with reference to the first group = dry, I # include an intercept column. …

edgeR glmTreat significance testing

updated 6.1 years ago • flemi221

gt; package for maize (as it is not available in the BSgenome package). > I have prepared the seed file and downloaded the fasta sequences and > then I proceeded to forge the genome. Then I quit R and followed the > manual...gt; > I am, as you might have already guessed, not a computer scientist and > have no clue whatsoever on what this means. > I am att…

Cancer BSgenome BSgenome Cancer BSgenome BSgenome

updated 13.0 years ago • Hervé Pagès

do that here. Because I use tissue cultures as follow: one big culture of each individual has been seeded in 13 different wells, and sampled over time. So I think that this is not independent, correct? I believe it would be pseudoreplicates

rain

updated 23 months ago • mata

<div class="preformatted"> Hi everybody ! I try to build a package to use oligo. so for that I use pdInfoBuilder and a bpmap file. I work on a tiling array from affymetrix. here is my sessionInfo() : > sessionInfo() R version 2.9.0 (2009-04-17) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF…

Annotation oligo pdInfoBuilder Annotation oligo pdInfoBuilder

updated 16.6 years ago • Elsa Aguera

lt;- sorted_RankgeneGLDS420 ####GO Gene Set Enrichment Analysis (set.seed(123) & gseGO(seed = TRUE)) set.seed(1234) goGLDS420.gsea <- gseGO(geneList = geneList.GLDS420, OrgDb = org.Mm.eg.db, seed = TRUE, ont = "ALL", keyType

clusterProfiler

updated 23 months ago • Max

of populating the SQLite Database, i then proceeded to build my custom annotationDBI.db package. *seed <- new("AnnDbPkgSeed", Package = "myCustomChip.db", Version = "1.0-0", PkgTemplate = "HUMANCHIP.DB", AnnObjPrefix = "myCustomChip...DBschema = "HUMANCHIP_DB", ) system("rm -rf myCustomChip.db") makeAnnDbPkg(seed, filename, des…

BiocViews Genetics Annotation GO Organism biocViews AnnotationDbi BiocViews BiocViews GO

updated 15.6 years ago • Julian Lee

I have placed all the chromosomes in their own FASTA files and gziped them. I then created a seed file like so: Package: BSgenome.Mtruncatula.JCVI.v4 Title: Full genome sequences for Medicago truncatula A17 (JCVI

bsgenome biostrings Gviz

updated 10.3 years ago • gtho123

time I run the example the permuted values stay fixed. Is there way to calculate values with random seeds? Thanks a lot, Stefanie. index <- c(rep(0,5),rep(1,5)) value <- c(3,6.5,2,1,1.5,6,9,8,0,3.5) expr <- t(matrix(value,10,2)) # a very correlated

multtest multtest

updated 22.6 years ago • Stefanie Scheid

<div class="preformatted"> Dear Xiaokuan slight differences can be expected due to the probe sampling that is used in the vsn2 method for AffyBatch to increase the speed of the computation. You can switch off the sampling e.g. by specifying "subsample=0" in the call to vsnrma. And you can make the sampling deterministic by calling set.seed before vsnrma. However, such differences should a…

probe probe

updated 15.5 years ago • Wolfgang Huber

C:\\Users\\hakim\\Desktop\\Bioinformatics_Thesis_Concordia_Microarry_Data\\Control" #setting seed for reproducibility set.seed(1) #listing the files from directory using special CEL file read function celList <- list.celfiles

microarray hugene20 limma oligo

updated 9.9 years ago • hakimelakhrass

full.names = TRUE) >> xys <- list.files(pattern = ".xys", full.names = TRUE)[1] >> seed <- new("NgsTilingPDInfoPkgSeed", >> ndfFile = ndf, xysFile = xys, >> posFile = pos, >> author = "Martin Aryee", >> version...HG 18", organism = "Human", >> species = "Homo sapiens") &a…

BiocViews Annotation Organism biocViews pdInfoBuilder charm BiocViews BiocViews Annotation

updated 13.7 years ago • zeynep özkeserli

I am working with __MEDIPS__ bioconductor. I was able to successfully create a custom BEE genome (I know its already there in MEDIPS, but for some reason I wanted to make a different one myself). The genome folder consists of 16 separate fasta files for each chromosomes named like chr1, chr2 and so on. The seed file is given below: <pre> Package: BSgenome.Amellifera.UCSC.apiMe1 Title: …

MEDIPS

updated 9.2 years ago • Vijay Lakhujani

<div class="preformatted"> Hello, one more error. It seems there are the commands reversed: 1. seed <- new("AnnDbPkgSeed", Package = paste(dbName, ".db",... 2. dbName <- .generateOrgDbName(genus, species) As for question why not to use...div class="preformatted"> Hello, one more error. It seems there are the commands reversed: 1. seed <- new("AnnDbPkgSeed", Packag…

BiocViews GO Organism ChipName biocViews BiocViews BiocViews GO Organism ChipName

updated 13.8 years ago • Guest User

Users/setsukosahara/Documents/data/Affy/oligo/pdInfoVignette/ AffyGene/MoGene-1_0-st-v1.r4.mps" > seed <- new("AffyGenePDInfoPkgSeed", + pgfFile = pgf, clfFile = clf, + probeFile = prob, transFile = transcript, coreMps = coreMps, author...email = "sahara at salk.edu", + biocViews = "AnnotationData", + organism = "Mouse", species = "mouse", + url = "http://www.salk.edu") > m…

BiocViews Annotation Organism biocViews oligo BiocViews BiocViews Annotation Organism

updated 14.6 years ago • Setsuko Sahara

nbsp;                          seed=100000)</code> then the output is <pre> Generating data from baseline model. Error in sample.int(length(x), size, replace, prob

polyester rnaseq simulation

updated 8.4 years ago • sseo2

<div class="preformatted">I really don't know if there is a problem or not for the background correction. I don't have anything to compare with it, at least there is no error displayed on the screen. For the flag, since I have a filter results on flag from Affy DMT, I compared it with the output of the Affy package and found the problem. Do you know other possible reasons for the inconsista…

Microarray affy Microarray affy

updated 21.8 years ago • Lizhe Xu

using 'limma' when I'm analysing some microarray data. If I run the below code WITHOUT setting a seed, I get slightly different values for the coefficients each time it's run; however this problem does not occur if I do set

updated 13.9 years ago • Guest User

div class="preformatted">SZSN Goes Through The Roof! UP 37.5% Shandong Zhouyuan Seed and Nursery Co., Ltd (SZSN) $0.33 UP 37.5% Brokers are grabbing up SZSN like crazy after two news releases this week. Huge expansion

updated 18.5 years ago • Theodore

I ran into a problem while running the **learn.bn()** function, and I got the error message candlist[I,1:2] subscript is out of bounds from running the toy example from the [pdf guide][1]. I also get this same error message from using the one.step.pigengene function by setting the parameter bnNum=10 as well. I've tried matching the bnlearn package version in the PDF guide and also tried using the…

Pigengene

updated 2.2 years ago • kjngo

<div class="preformatted">Hi, I need to re-map the probe sequences of the Affymetrix Bovine genome array to a recent draft sequence of the sheep genome (please, don't ask why...). As a first step, I successfully created a new BSgenome package from a seed file, listing individual chromosomes as 'seqnames' and unmapped, and two multiple sequence fasta files as 'mseqnames', as...please, don't…

BSgenome probe BSgenome BSgenome probe BSgenome

updated 13.1 years ago • David Iles

read.csv(paste(base_dir, "/HTA-2_0.na33.hg19.probeset.csv", sep=""), skip=14, header=T) > > seed = new("AffyExonPDInfoPkgSeed", + pgfFile = pgf, + clfFile = clf, + probeFile = prob, + coreMps = core_mps, + extendedMps = extended_mps, + fullMps...genomebuild = "GRCh37", + organism = "Human",…

BiocViews Annotation Organism biocViews oligo oligoClasses BiocViews BiocViews Annotation

updated 10.7 years ago • Guilherme Rocha

style="background-color:Yellow"><code>library(BSgenome)<br/> > forgeBSgenomeDataPkg("path/to/my/seed")</code></span> it working and creating<code> <strong>the single_sequences.2bit</strong></code> the when i run the second command

bsgenome

updated 7.2 years ago • oussama.badad

<div class="preformatted"> I am writing to inquire about independent filtering for my large RNA- seq dataset. I have around 55,000 genes (raw gene counts) RNA sequencing data from 91 libraries/samples, consisting of 3 biological replicates for 4 different genotypes on germinating seeds. I am currently working on differential expression and subsequently transcriptomic network analysis for th…

Normalization GO Network HTSFilter DESeq2 Normalization GO Network HTSFilter DESeq2

updated 12.1 years ago • Guest User

pmFeatures"]], tiledRegionPmFeatureSchema[["col2type"]], !quiet) 2: makePdInfoPackage(seed, destDir = ".") 1: makePdInfoPackage(seed, destDir = ".") > sessionInfo() R version 2.15.2 Patched (2013-02-08 r61876) Platform: x86_64...there is no package called ?pd.100929.hg19.deluxe.prom.meth.hx1? I read the pdInfoBuilder package reference, charm reference. I am not able to find a reply…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.4 years ago • Nitesh Turaga

gt; traceback() 5: .makeAnnDbPkg(x, dbfile, dest_dir = ".", no.man = FALSE, ...) 4: makeAnnDbPkg(seed, file.path(outputDir, paste0(prefix, ".sqlite")), dest_dir = outputDir) 3: makeAnnDbPkg(seed, file.path(outputDir, paste0(prefix

GO Cancer ChipName probe affy GO Cancer ChipName probe affy

updated 13.1 years ago • Guest User

Hello, everyone! 1. I got the error ___'Error in if (abs(max.ES) > abs(min.ES)) { :  ___ ___missing value where TRUE/FALSE needed' ___ when running gseaplot() to visualize the GSEA result.   2. I run the code '_gseaplot(gsea, geneSetID = "mmu03013")'  _where gsea is a__ gseaResult__ object. The class of&nbsp…

gsea clusterprofiler

updated 8.1 years ago • giuseppe0525

lt;- get_default_training_options(MOFAobject) train_opts$convergence_mode <- "slow" train_opts$seed <- 42 MOFAobject <- prepare_mofa(MOFAobject, data_options = data_opts, model_options = model_opts, training_options

MOFA2

updated 2.7 years ago • Dan

<div class="preformatted"> Hi, Lana, There are two points to be cared in this procedure. One is that probe-masking should be done after the quantile normalization. RMA quantile normalization does not provide what you want if there are some NA values. The other point is to specify "na.rm=TRUE" in the step of summarization. Unfortunately, current version of C-coded rma() function does not su…

Normalization Normalization

updated 20.9 years ago • t-kawai@hhc.eisai.co.jp

i (number of iterations) 100000 -b (burnin) 50000 -s (seed random init) 1657784617 -p (number of processes (CPU)) 1 -x (genotype file) Genidentity.lfmm -v (variable file) variables.env

lfmm LEA

updated 4.6 years ago • valentinarov

I'm trying to design a CRISPR gRNA and search for off-targets with CRISPRseek. My organism has a very rough draft genome that is organized into ~160,000 scaffolds. I've been able...I'm trying to design a CRISPR gRNA and search for off-targets with CRISPRseek. My organism has a very rough draft genome that is organized into ~160,000 scaffolds. I've been able to...I placed a single scaffold into …

crisprseek grna searching bsgenome forge offtarget analysis

updated 9.6 years ago • rajewski23

correspond to each other as they were sampled at the same intervals beginning at the same time after seeding. Currently I am using the following to test for differential expression: <pre> dds = DESeqDataSetFromHTSeqCount(sampleTable

deseq2 sva

updated 9.1 years ago • brookb

500, maxCount = 10000, subsample = TRUE, nbrSubsample = 200, seed = 1, minSize = NULL, maxSize = NULL, verbose = FALSE) { ## Define the temporary directory where the ensDb object will be saved tmpdir...if (verbose) message("Subsampling genes for fitting bias model...") …

Alpine jcc

updated 6.3 years ago • bioinagesh

Hello, I am working with a lesser-known fungal species that has a GenBank reference assembly, but it does not have RefSeq information or UCSC annotations. I can generate a txdb object from the .GFF...Hello, I am working with a lesser-known fungal species that has a GenBank reference assembly, but it does not have RefSeq information or UCSC annotations. I can generate a txdb object from the .G…

OrgDb BSgenome

updated 2.2 years ago • mat149

<div class="preformatted">Hi list, This wasn't sent out with a none registered ids. I have a problem with forging a new BSgenome data package. The sequence data file is clof.v3.fa and the mask file is clof.v3.fa.masked. Below are seed file, command, error and sessioninfo. Your help will be much appreciated. Thanks a lot, Steve Package: BSgenome.Clof.yu.v3 Title: Clof (insects) full genom…

BSgenome Biostrings BSgenome BSgenome Biostrings BSgenome

updated 14.9 years ago • Steve Shen

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Pathways PROcess BRAIN Pathways PROcess BRAIN

updated 18.5 years ago • Neddy

a set (as big as posssible) of experimentally Validated miRNAs from miRecords with their relative target genes and the 3'UTR sequences., limited to Homo sapiens. The XLS file from miRecords related the miRNA identier ("hsa-miR...xxx) with its target genes identifier. I never found a clear way to download the miRNA sequence and the relative target 3'UTR sequence from...miRNAs whose identifiers di…

Transcription miRNA Homo sapiens biomaRt Transcription miRNA Homo sapiens biomaRt

updated 16.3 years ago • mauede@alice.it

library(rGADEM) library(BSgenome.Hsapiens.UCSC.hg38) novel_motifs <- GADEM(dataRange_resized, seed = 2, nmotifs = 10, genome = Hsapiens) Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord

rGADEM

updated 3.2 years ago • Nils.Rother

I have 6 .fa files named SP_chr01.fa --> 06 located into seqs folder. ``` ##data.frame for seed pombe_dataframe <- data.frame( Package = "BSgenome.Spombe.Pombase.ASM294v2", Title = "Full genome sequence for Schizosaccharomyces...indent = 0.1*getOption("width"), width = 0.9*getOption("width"), keep.white = NULL) ##Forge the target package; lead the way to the .dcf file …

bsgenome MutationalPatterns

updated 5.7 years ago • sibyl.bertrand

N=length(YY1))<br/>     pt1 <- peakPermTest(YY1, TEAD4, pool=pool, seed=1, force.parallel=<strong>FALSE</strong>)<br/>     plot(pt1)</code> In my case, I don't want to do any subset of <span

permutation pool chippeakanno

updated 7.5 years ago • ge2sasag

message when I try to make the annotation for this platform using pdInfoBuild. In pdInfoBuilder Reference Manual (June 5, 2013), under the NgsExpressionPDInfoPkgSeed method, there is a slot for pairFile, although, showClasses...Yanmin Microarray RAW/GSM618107_14418002_532.xys" But, doing this resulted in an error message: seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile = ndf, xysFile =…

Microarray Annotation Organism annotate pdInfoBuilder Microarray Annotation Organism

updated 12.6 years ago • Guest User

div class="preformatted"> Hello. You have to remove the random seed using: if(exists(".Random.seed")) rm(.Random.seed) before you run the impute.knn function if you are using a Windows machine

Clustering impute Clustering impute

updated 20.7 years ago • Marcus

mc.cores=cores, groupInfo = groups, cutoffFstat = fstat, cutoffType = 'manual', nPermute = perms, seeds = 19731107 + seq_len(perms), lowMemDir = file.path(tempdir(), currentChrom), BPPARAM.custom = MulticoreParam(workers = cores...mc.cores=cores, groupInfo = groups, cutoffFstat = fstat, cutoffType = 'manual', nPermute = perms, seeds = 19731107 + seq_len(perms), lowMemDir = file.path(tempdir(), cu…

derfinder

updated 10.8 years ago • jessica.hekman

Z + B, covariates) ``` In this case, the model matrix will be the following (I set the random seed to 1): ```r (Intercept) A Z B 1 1 0 1 0 2 1 1 2 0 3 1 0 2 0 4 1 0 2 0 5 1 1 2 0 6 1 0 3 0 7 1 0 1 0 8 1 0 3 1 9 1 1 1 1 10 1 1 1 1 11 1 0 1 1 12 1 0 1…

ALDEx2 modelmatrix covariates

updated 2.5 years ago • amir

230, maxLength = 7000, minCount = 10, maxCount = 10000, subsample = TRUE, nbrSubsample = 30, seed = 1, minSize = NULL, maxSize = 220, verbose = TRUE) Creating TxDb object... Importing GTF file ... Import genomic features from the file

genomicfeatures

updated 6.4 years ago • bioinagesh

Leo -- thanks for your recent help with fullCoverage() in derfinder. After your updates, that function began 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.   R 3.1.1 Bioconductor version 3.0 (Bio…

derfinder

updated 11.2 years ago • jessica.hekman

Batch size: 50 *** Optimal acceptance ratio: 0.44 *** Name of output directory: ./run.3 *** Seed for random number generator: 192492 *** CEL files: WTampC_rep1.cel, WTampC_rep2.cel, WTampC_rep3.cel, WTampM_rep1.cel

probe probe

updated 18.0 years ago • Louisa A Rispoli/AS/EXP/UTIA