Bioconductor Forum

a href="http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/latest_phaseIII_ncbi_b36/plink_format/" target="_blank">http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/latest\_phaseIII\_ncbi\_b36/plink\_format/</a>) The copy...ca1=CA(cnset, j = 1)[, 1] cb1=CB(cnset, j = 1)[, 1] table(snp_data$isSnp[<a href="http://is.na" target="_blank">is.na</a>(ca1)]) # FALSE TRUE # 94…

crlmm copynumber

updated 10.8 years ago • kforner

<div class="preformatted"> Thank you for your comment, Laurent. Yes, your way is a smart way to remove in-file MASKS probes. By the way, '.MSK' files are provided by Affymetrix or created by the indivisual user which contains probe cells to be masked in the analysis step. Old design chip like Hu6800 has a lot of masking probes to remove cross-hybridization data. Detail description can be …

Normalization Preprocessing hu6800 probe Normalization Preprocessing hu6800 probe

updated 22.2 years ago • t-kawai@hhc.eisai.co.jp

<div class="preformatted">Dear Benilton, thanks for this first draft support for the HTA 2.0 chip. I tried to follow your workflow using your annotation package specific for HTA or one built through pdInfoBuilder. For both I can not use the package pd.hta.2.0, see below. > library(oligo) > install.packages("C:/Users/JP/Desktop/HTA/pd.hta.2.0.zip", repos = NULL) > li…

Annotation pdInfoBuilder Annotation pdInfoBuilder

updated 9.5 years ago • Johann Pellet

We are performing RNA-seq analysis in R using Rsubread and edgeR. We would like to be able to create a design matrix that allows our samples to be paired together. We have been following the edgeR quasilikelihood pipeline (Link: [Chen, Lu and Smith, 2020][1]. We modified this pipeline to use glmLRT as opposed to the glmQLRT and then attempted to include multiple parameters in our design matrix, …

edgeR pairedsamples designmatrix

updated 4.9 years ago • sfidemw

Hi I would like to perform de novo mutational signature extraction. I am trying to follow the vignette of the MutationalPattern package. I managed to create the matrix for my samples. However, I encounter problems when I try to estiamte the number of mutational signatures in my samples. Here my code and corresponding errors: estimate<- nmf(mut_mat, rank=2:5, method="brunet", nru…

MutationalPatterns NMF

updated 6.6 years ago • TRASA

mnt/Prairie_Vole_Data/Arjen_Folder/Arjen/genomefiles_mo/NCBI/BSgenome.Mochrogaster.NCBI.micOch1.0-seed")``` **but keep getting errors, either this one:** ``` Error in .make_Seqinfo_from_genome(genome) : "MicOch1.0" is not a registered NCBI...removing the seqnames field from the seedfile, but then I get the first error.** **Here is my seed file:** ``` Package: BSgenome.Mochrogaster.NCBI.MicO…

BSgenome microtus forging

updated 5.1 years ago • A.J.

3 temperature points (K, P1, P2) and 2 biological replicates(72 samples in total). "Org" and "K" are reference levels for seed lot & temperature respectively. Here is the col data. ID is the grouped variable of seedlot, time...at a temp between seedlots eg: test DE genes between HC1_P1 and OC1_P1 with HC1_K and OC1_K as reference levels respectively. How do i set up a contrast matrix for…

timecourse DESeq2 RNASeq

updated 4.3 years ago • Akhil

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

hugene20 microarray limma limma paired analysis oligo

updated 9.9 years ago • hakimelakhrass

<div class="preformatted">Hi Peter, I'm still having some difficulty with the first step of BitSeq. I made myself a mini dataset with just 5 million reads so that I could run everything in my R console without writing and R script and submitting to the cluster (just until I know what I'm doing) but, I got this error: Error in getMeanVariance(c(outFile), meanFile, log = log, pretend = prete…

Alignment PROcess BitSeq Alignment PROcess BitSeq

updated 12.8 years ago • Maayan Kreitzman

<div class="preformatted">Hi Julian, The 1st thing to note is that you cannot actually produce a version 1.0 schema at this time. You can only make a 2.1 version schema. The older schemas are unsupported, and only the files remain for people who might encounter an older database. To answer your question about ACCNUM, this is a mapping that is normally used to store the ID that was origi…

BiocViews Genetics Annotation GO Organism probe biocViews AnnotationDbi BiocViews GO

updated 15.6 years ago • Marc Carlson

Hi, I am running (to me) identical code for some clustering but despite fixed seeds it is inconsistent when using either lapply or bplapply: Any idea what is happening? ``` suppressMessages({ library(BiocParallel

scran BiocParallel bluster

updated 20 months ago • ATpoint

easier sorting later > rownames(khan.expr) <- paste0("Gene", 1:2308) #Check that no random seed exists prior to running imputation on the data set as is > if(exists(".Random.seed")) rm(.Random.seed) #Run imputation > Result1_OriginalOrder

impute

updated 22 months ago • Tamara

file and the second column contains transcript names. (all BitSeq output keeps the same order of reference sequences) Also, I think the first element of the result 'res_A08485$exp' contains mean expression and variance...Homo_sapiens.GRCh37.69. cdna.all.fa", >> outPrefix="A08485_gr4.sam_mini.run1", log=TRUE, seed=47, verbose=TRUE); >> >> Which should cre…

Alignment PROcess BitSeq Alignment PROcess BitSeq

updated 12.8 years ago • Peter Glaus

Hi! I am not sure if I misunderstand how GSEA works or I have an error in my GSEA analysis. I am using clusterProfiler (gseKEGG function). Input data: - output from DESeq2 ("control vs mutant" and "mutant vs control" --> I just set the contrast in both directions. it was the same input in DESeq2) - ranking of genes based on log2foldchange (sign of log2FC is of course inverse for "control…

clusterProfiler gseKEGG

updated 21 months ago • andromeda

GLCHR01 through GLCHR05) and a few extra fragments (ex: AACB02000013_frag). Below is the seed file used to forge/build the genome: ``` Package: BSgenome.Glamblia.GiardiaDB.35 Title: Genome sequence for Giardia lamblia

cleanUpdTSeq BSgenome BSgenomeForge

updated 6.8 years ago • danielle.bilodeau

Dear Bioconductor Community, the reference manual (October, 21, 2014) of the bioconductor trigger package states that it is doing calculations in parallel...Dear Bioconductor Community, the reference manual (October, 21, 2014) of the bioconductor trigger package states that it is doing calculations in parallel at...Should I install a different parallelization package other than doMC? Do I someh…

trigger parallel processing multicore

updated 11.2 years ago • affennacken

8x60K", fileName = agilent_IDs, metaDataSrc = myMeta, baseMapType = "eg", outputDir = tmpout) >seed <- new("AnnDbPkgSeed", Package = "Agilent 8x60K.db", Version = "1.0.0", PkgTemplate = "HUMANCHIP.DB", AnnObjPrefix = "Agilent 8x60K...gt;makeAnnDbPkg(seed, file.path(tmpout, "Agilent 8x60K.sqlite"), dest_dir = tmpout) simplifying probes table dropping redundant data Creating...from …

Annotation probe affy AnnotationDbi Agi4x44PreProcess Annotation probe affy AnnotationDbi

updated 13.5 years ago • Karthik K N

<div class="preformatted">Just wondering if anyone has had any luck creating annotation packages for the HTA 2.0 chip? Best, Stephen On Tue, Sep 10, 2013 at 8:24 PM, Mark Cowley <m.cowley@garvan.org.au> wrote: > Hi Vincent & Benilton, > Myself and Philip de Groot have independently tried to create the > pd.hta.2.0.db overnight with the same error (thou…

BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews

updated 12.1 years ago • Stephen Turner

does not play well with Matrix or irlba. I am running ``` sce <- decontX(sce, seed = 12345) ``` ``` ```My output message is. -------------------------------------------------- Starting DecontX -------------------------------------------------- Thu Nov 9 15:11:36 2023 .. Analyzing all cells Thu Nov 9 15:11:36 2023 .... Converting

decontX celda

updated 2.2 years ago • Shea

277278 303634 442510 414728 ... > combp(nat_vs_art_combp_filter,dist.cutoff=1000,bin.size=310,seed=0.5, + region_plot=TRUE,mht_plot=TRUE,nCores=10) Error in if (any(p.stouffer > 0.05)) { : missing value where TRUE/FALSE needed

ENmix

updated 5.2 years ago • mwjnorris

but had the same problem with R 2.10/BioC 2.5. 1. I had to specify the coreMps when creating the seed. Otherwise got a "coreMps" not found error, which was different from what the manual says. I did not see any information about

Annotation affy oligo pdInfoBuilder Annotation affy oligo pdInfoBuilder

updated 15.5 years ago • He, Yiwen NIH/CIT

Hello, today I had some problem in DE analysis results replication. I analyzed the same dataset, with exactly the same code, same DESeq2 version but i got different results in a comparison. How could it be? ```r dds_stage <- DESeqDataSetFromTximport(cur_txi, cur_sampleTable, ~uid+stage) ``` The dataset is composed by 150 tumoral and matched-normal samples (for this reason I used the d…

RNASeqData DESeq2

updated 2.5 years ago • Matteo

0 [100000,] 0 0 0 0 . 0 0 0 0 > seed(mat) An object of class "HDF5ArraySeed" Slot "filepath": [1] "/home/simulation/mockdata/mockdata_consensus_counts.h5" Slot

DelayedArray HDF5Array

updated 4.6 years ago • Pedro Baldoni

**Overview** **Cures Start Here.** At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the development of immunotherapy, which harnesses the…

biostatistics bioinformatics computational biology bioconductor Job

updated 6.2 years ago • Fred Hutch (Recruiting)

Hi to the Bioconductor community, I have been in the process of forging many genomes and found that after the upgrade of R to a version like R version 3.2.3 (2015-12-10), the use of the forgeBSgenomeDataPkg command originates a error that does not occur when I use a R version like R version 3.0.2 (2013-09-25). I leave bellow the output I get when I start to forge a particular genome, with the s…

bsgenome forge

updated 9.5 years ago • pj dias

levels = c("WT", "S")) ## DESeq2 pipeline # set.seed(2020) # set seed deseq <- DESeqDataSetFromMatrix(countData = cds_ord, colData = metaData, design = ~ Population + Time + Population:Time) # import

deseq2 RNA

updated 5.7 years ago • agsousa

tmp_class, x) : all elements in 'x' must be DNAString objects</pre> This is the seed file content: <pre> Package: BSgenome.Zmays.EnsemblPlants.AGPv4r32 Title: Zea mays (EnsemblPlants AGPv4 release 32

BSgenome

updated 9.2 years ago • ROka

_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ then i created the seed file and forge the bsgenome package as the instructions. there are actually no errors when checking the built package

bsgenome txdb promoter

updated 9.9 years ago • sekawaiwai2006

problem while forging the genome with bare sequences. What did I miss(understand) in the manual? My seed file: Package: BSgenome.Dmelanogaster.UCSC.dm6.masked Title: Full masked genome sequences for Drosophila melanogaster...from the UCSC site. <pre> forgeMaskedBSgenomeDataPkg("BSgenome.Dmelanogaster.UCSC.dm6.masked-seed")</pre> Creating package in ./BSgenome.Dmelanogaster.UCS…

bsgenome drosophila melanogaster bsgnome forge

updated 9.1 years ago • nadia.goue

one appears to be needed according to section 2.3 of ggbio vignette dated August 26, 2014 to add a reference track eventually to be used in an 'overview plot' (chpt 4 of the vignette). Problem: I received the following error message...Users/bterry/macbookpro2014/keenanres/Sitalica/packs/sitalica22/BSgenome.Sitalica.Ensembl.22-seed") Creating package in ./BSgenome.Sitalica.Ensembl.22 Error …

bsgenome ggbio

updated 6.2 years ago • pterry

A: mauede@alice.it Cc: Bioconductor List Oggetto: Re: [BioC] R: How can I trace back transcription target genes from the miRNAs file downloadable from miRbase ? Hi, Maura, You can possibly find the microRNA package useful...your task. It contains the database from miRBase along with the target genes. You can then use this database to find the sequence using biomaRt. This package does not hav…

Transcription miRNA Cancer Homo sapiens biomaRt microRNA Transcription miRNA Cancer

updated 16.3 years ago • mauede@alice.it

chrY LN:59373566 @PG ID:TopHat VN:2.0.7 CL:/opt/tophat-2.0.7.Linux_x86_64/tophat --seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 25 --transcriptome-index /srv/data/indexes/gencode.v19.annotation.basic_only

riboSeqR

updated 11.3 years ago • Laura.Fancello

TRUE) sce <- cluster(sce, features = "state", xdim = 10, ydim = 10, maxK = 20, seed = 1234) sce <- runDR(sce, "UMAP", cells = 1e3, features = "state") sce <- runDR(sce, "TSNE", cells = 500, features = "state") ``` This is the resulting

CATALYST

updated 3.4 years ago • David

in BioMart bm <- getBM(attributes = "hgnc_symbol", mart = ensembl)$hgnc_symbol ## set seed set.seed(2021) ## build a control with baseline across all genes, ## build a treatment case with a random uniform distribution

pathview org.Hs.eg.db

updated 4.7 years ago • Rodrigo

within your own lab. That would suggest batches of plants grown separately from separate batches of seed. The best plan is a randomized complete block design, with every condition sampled in every block. If the conditions are

Normalization probe affy affyPLM Normalization probe affy affyPLM

updated 20.0 years ago • Naomi Altman

I noticed that if I run enrich_motif with background sequences that were shuffled different RNG seed values, the number of motif hits in the TARGET group of sequences is slightly different. I do also see this slight variation...in the background set (this was expected) but I was not expecting this to also happen in the target group of sequences since they are the same in each run. ```r # Get ta…

universalmotif scanning enrich_motifs PWM

updated 4.0 years ago • alexandre.blais

T)[1] > > > mps <- list.files(baseDir, pattern = ".mps$",full.names=T)[1] > > > seed <- new("AffyGenePDInfoPkgSeed", > > > pgfFile = pgf, clfFile = clf, > > > probeFile = prob, > > > coreMps=mps, author = "Mark...genomebuild = "NCBI Build 37", > > > organ…

BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews

updated 11.7 years ago • Elena Serrano

<div class="preformatted">Hi there, I am trying to create one of the genome packages for the SK1 strain of S. cerevisiae. I thought it was going okay and the guide is very clear. When it comes to checking the package there were a few error messages. In the guide it said ignore messages so I plugged on and the installation went through okay. I cannot load up the package now though. Im using…

Saccharomyces cerevisiae BSgenome Biostrings BSgenome Saccharomyces cerevisiae BSgenome

updated 11.6 years ago • Guest User

T)[1] > > > mps <- list.files(baseDir, pattern = ".mps$",full.names=T)[1] > > > seed <- new("AffyGenePDInfoPkgSeed", > > > pgfFile = pgf, clfFile = clf, > > > probeFile = prob, > > > coreMps=mps, author = "Mark...genomebuild = "NCBI Build 37", > > > organ…

BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews

updated 12.0 years ago • Elena Serrano

gt;> tiledRegionPmFeatureSchema[["col2type"]], !quiet) >> 2: makePdInfoPackage(seed, destDir = ".") >> 1: makePdInfoPackage(seed, destDir = ".") >>> sessionInfo() >> R version 2.15.2 Patched (2013-02-08 r61876) &gt...pd.100929.hg19.deluxe.prom.meth.hx1? >> >> >> I read the pd…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.4 years ago • Nitesh Turaga

Hi, I am new to RNA seq and seq data analysis. I want to use DESeq2 to extract differential expression data for cells (from three donors) seeded on two different scaffolds (scaffold 1 and 2) across three different time points and compare them with an industry standard...analysis. I want to use DESeq2 to extract differential expression data for cells (from three donors) seeded on two different …

rna-seq deseq2 deseq R

updated 7.4 years ago • arun.thirumaran

a linux-server, but I think this is not the problem, since the fasta files were loaded. This is my seed-file: Package: BSgenome.Hsapiens.NCBI.GRCh38.p11 Title: Homo Sapiens full genome for RRBS (NCBI version GRCh38.p11..._spike-in\_CC\_100") circ\_seqs: "NC\_012920.1" seqs\_srcdir: /home/lmoebus/mountrz\_work\_zfs/references/BSgenome\_R\_package/seqs\_srcdir seqfiles\_suffix: .…

bsgenome forge TwoBits_export

updated 8.3 years ago • stu111538

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

derfinder

updated 10.7 years ago • jessica.hekman

Hello, I have successfully run derfinder following the tutorial on some human data, but now I am getting an error when trying to go through the same process with some mouse data. Any help would be appreciated. Thanks, Paul Schaughency Here is the relevant log: <pre> > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.0 (BiocInstaller 1.16.4), ?biocLite for …

derfinder

updated 10.6 years ago • pschaugh

gt; tiledRegionPmFeatureSchema[["col2type"]], !quiet) > >>> 2: makePdInfoPackage(seed, destDir = ".") > >>> 1: makePdInfoPackage(seed, destDir = ".") > >>>> sessionInfo() > >>> R version 2.15.2 Patched (2013...gt; >>> > >>> …

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.3 years ago • Benilton Carvalho

for the featureSet table... This table stores > the information for "genes" (or whatever the target for this > particular array is)... so, it is unlikely that you have a microarray > with only 2 "target units"... I'd expect something...gt; thousands... > > pdInfoBuilder uses the information in SEQ_ID (in the NDF) to get the > target information (i.e., the…

Microarray Annotation GO Organism probe annotate limma convert pdInfoBuilder sva GO sva

updated 12.6 years ago • Johnson, Franklin Theodore

wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not...Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison...storing and manipulating short genomic a…

BiocViews aCGH SNP Sequencing RNASeq ChIPSeq miRNA Microarray qPCR Metabolomics Coverage

updated 11.7 years ago • Dan Tenenbaum

sequencing. - BiSeq: The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced- representation bisulfite sequencing (RRBS) data. In particular, it...are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data s…

BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO

updated 10.5 years ago • Dan Tenenbaum

Sean Davis) 9. Interpreting DESeq2 results (Michael Muratet) 10. identifying drosophila miRNA targets (Fiona Ingleby) 11. Re: identifying drosophila miRNA targets (James W. MacDonald) 12. Re: Limit on number of sequence files...layout # Returns data object with targets, genes and printer layout ###################################################################### ######### parse &lt…

miRNA Annotation Normalization Visualization Clustering Infrastructure Cancer BSgenome vsn

updated 12.8 years ago • Matthew Thornton

description I now see some rationale about this normalization, when all Red chanels contoined common reference (which is commercial "universal human reference"). However, question remains, what kind of plots, metrics are useful...information on Agilent's eArray web site: > earray.chem.agilent.com > > Q5: for a common reference design, dye swaps are not required and > I…

SNP Transcription Sequencing RNASeq miRNA Microarray Annotation Normalization GO Cancer

updated 13.9 years ago • Polikepahad, Sumanth

Array","MANUFACTURERURL"="http://www.affymetrix.com "),baseMapType="eg",outputDir="primeview"); # seed<-new("AnnDbPkgSeed",Package = "primeview.db",Version="1.0.0",PkgTemplate="HUMANCHIP.DB",AnnObjPrefix ="primeview"); # makeAnnDbPkg...seed,dbfile=file.path("primeview","primeview.sqlite"),des t_dir="primeview"); Error in makeAnnDbPkg(seed, file.path("primeview

Annotation Annotation

updated 12.8 years ago • wang peter