Bioconductor Forum

clf",full.names = TRUE)) (prob <- list.files(baseDir, pattern = ".probeset.csv",full.names = TRUE)) seed <- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile = clf,probeFile = prob, author = "Javier",email = "email",biocViews = "AnnotationData...genomebuild = "NCBI Build 36",organism = "Human", species = "Homo Sapiens",url = "") makePdInfoPackage(seed, destDir = ".") And I install…

Preprocessing cdf oligo oneChannelGUI Preprocessing cdf oligo oneChannelGUI

updated 16.2 years ago • Javier Pérez Florido

nbsp;                       writeTable = T, seed=seed,plot="pdf") I got an error: Error in ConsensusClusterPlus(d, maxK = maxK, reps = 50, pItem = 0.8,  :    d must be a matrix

bioconductor clustering consensusclusterplus

updated 8.9 years ago • kyn

lt;- FlowSOM(fileName, compensate=TRUE,transform=TRUE, scale=TRUE,colsToUse=c(9,12,14:18),nClus = 10, seed=1) # Have a look at the resulting tree # PlotStars(flowSOM.res[[1]],backgroundValues = as.factor(flowSOM.res[[2]])) # Select all cells...flowSOM.res <- FlowSOM(MYFlowSET, scale=TRUE,colsToUse=c(9,12,14:18),nClus = 10, seed=1) At this point, I am lost. I would like to extract,…

flowcytometry flowSOM flowSET flowFrame

updated 6.7 years ago • fabrizio.benedetti.82

Uniprot Appending Metadata simplifying probes table dropping redundant data Error in makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""), : subscript out of bounds ######################## ######################## > traceback() 4: makeAnnDbPkg(seed, paste(outputDir, "/", prefix...sqlite", sep = ""), dest_dir = outputDir) 3: makeAnnDbPkg(seed, paste(outputDir, …

GO ChipName probe affy GO ChipName probe affy

updated 13.3 years ago • Guest User

following error (which I am unsure how to fix): Thanks for any suggestions. Regards, Paul > seed <- new("AffyGenePDInfoPkgSeed",pgfFile = pgf, clfFile = clf,probeFile = probe, transFile = trans, coreMps = core) > > makePdInfoPackage...seed, destDir = ".") ====================================================================== ========================================…

Annotation probe Annotation probe

updated 12.6 years ago • Guest User

memory... Error in smartReadXYS(filenames, sampleNames) : negative extents to matrix Any clues? My best regards for all PS: Here is my entire pipeline. >source("http://bioconductor.org/biocLite.R") >library(pdInfoBuilder...ndf',full.names=T) >filename_xys <- list.files('.',pattern=".xys",full.names=T)[1] >seed <- new("NgsExpressionPDInfoPkgSeed", nd…

Microarray Microarray

updated 15.5 years ago • Marcelo Brandão

transcript <- "HTA-2_0.na33.hg19.transcript.csv" mps <- "HTA-2_0.r1.Psrs.mps" seed <- new("AffyGenePDInfoPkgSeed", pgfFile=pgf, clfFile=clf, probeFile=probe, transFile=transcript, coreMps=mps) makePdInfoPackage...seed, destDir=".", unlink=TRUE) ====================================================================== ========== Building annotat…

Annotation affy Annotation affy

updated 10.7 years ago • He, Yiwen NIH/CIT

I'm looking to parallelise 2 sva functions: __num.sv:__ where B=20 indicates 20 permutations <pre> <a href="http://num.sv">num.sv</a>(dat, mod, method="be", vfilter=NULL, B=20, seed=NULL)</pre> __sva:__ where B=5 is the no. iterations of the irw algorithm <pre> sva(dat, mod, mod0=NULL, <a href="http://n.sv...20 pe…

sva methylation

updated 8.6 years ago • stewart999

learnt <- learn.bn( pigengene = pigengene, bnPath = file.path(saveDir, "bn"), bnNum = 10, seed = 1, verbose = 4, onCluster = FALSE ) learn.bn() with bnNum= 10 started at: 2024-12-13 14:24:37.574856 Start learning 10 BNs for module...entry [[1]] learn.bn(pigengene = pigengene, bnPath = file.path(saveDir, "bn"), bnNum = 10, seed = 1, verbose = 4, onCluster =…

Pigengene

updated 12 months ago • Thomas

msgbsR/BSgenome.Rhinella.marina/caneToad_seed') Error in .readSeedFile(x, verbose = verbose) : seed file '/Users/jiazhou/Box/methylation_analysis/msgbsR/BSgenome.Rhinella.marina/caneToad_seed' must have exactly...1 record ``` I write the information for the seed file in txt format and used write.dcf function to generate dcf format. ``` > CaneToad_seed <- read.delim("ca…

software error

updated 5.3 years ago • jiazhou0116

reference.class=ref.class, plot.label=plot.label, rand=SEED) save(r.forest, file=paste("backRF",SEED,".RData",sep="")) } So it seems that specifying both "mtry" and "var.numbers" for RF.wrap is allowed

Classification MCRestimate Classification MCRestimate

updated 13.4 years ago • Guest User

SigG = mulCalc(mulcomScores , m=0.3 , t=3) permutation = mulPerm(CtvT1, groups, np = 100, seed=1) diffg <- mulDiff(CtvT1, permutation, m = 0.3, t = 3, ind = 1)</pre> The thing is that I'm getting "Error in input files" at mulDiff execution

mulcom error differential gene expression microarray

updated 8.8 years ago • arronar

<div class="preformatted">Paul Shannon <pshannon ...="" at=""> writes: > > I offer below a short example of using rGADEM with MotifDb which you may find useful. > > The example motivates and then demonstrates "seeded" search, in which a candidate TF is provided to > rGADEM. (The rGADEM vignette illustrates the simpler task of de novo motif search. …

rGADEM MotIV MotifDb rGADEM MotIV MotifDb

updated 11.8 years ago • Bahar

pattern = ".xys",full.names = TRUE) pos <- list.files(baseDir, pattern = ".pos",full.names = TRUE) seed <- new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile = xys, posFile = pos, author = "Andrew Beggs", email = "a.beggs at bham.ac.uk...biocViews = "AnnotationData",genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens", url = "http://www.biostat.jhsph.edu/~bcarvalh") …

BiocViews biocViews pdInfoBuilder BiocViews BiocViews biocViews pdInfoBuilder

updated 13.2 years ago • Guest User

3, dat2 is 4, dat3 is 5. Could Wolfgang or someone explain this to me? Is there a way to seed a value and make the results same? Thank you. Xiaokuan [[alternative HTML version deleted]] </div

probe probe

updated 15.5 years ago • Xiaokuan Wei

data <- AddModuleScore( object =data, features = angio_Features, ctrl = 5, name = 'angio_score', seed = 1 )` #add angio score on each sample Then I create the monocle object "monocle_data", Now I use plot_cell_trajectory to check

scRNA seq monocle

updated 5.5 years ago • initialqy

de.prob = c(0.05, 0.05, 0.05, 0.05, 0.05), de.facLoc = 3, de.facScale = 0, dropout.present = TRUE, seed = 1) `` Since the update to R version 3.4 and the newest Bioconductor version this code gives an error: Error in checkSlotAssignment

splatter

updated 8.2 years ago • luke.zappia

wondering if some documentation somewhere lists which criteria were used to include miRNA -> mRNA target sets in the RmiR.Hs.miRNA package? For example, say for TargetScan , which version of TargetScan was used to calculate...targets? What were the cutoff's for PCT, Total Context Score, conservation and which seed matches were included? Similar questions

miRNA RmiR miRNA RmiR

updated 14.7 years ago • Paul Geeleher

<div class="preformatted">Hi all, Thank you all for your previous help. I really appreciate your assistance! When I follow the HowTo I am able to apply the norm2Filter to the > fs <- read.flowSet(path = system.file("extdata", "compdata", "data", package = "flowCore"), name.keyword = "SAMPLE ID", phenoData = list(name = "SAMPLE ID", Filename = "$FIL")) > morphGate &am…

updated 18.4 years ago • M. Jankowski

didn't seem to work (code below). Many thanks, Cei library(AffyCompatible) library(pdInfoBuilder) seed <- new("AffyGenePDInfoPkgSeed", pgfFile = "MoGene-1_0-st-v1.r4.pgf", clfFile = "MoGene-1_0-st-v1.r4.clf", probeFile = "MoGene-1_0...genomebuild = "mm9", organism = "Mus musculus", species = "Mouse") makePdInfoPackage(seed, destDir=".") ================================…

BiocViews Annotation Organism affy PROcess biocViews BiocViews BiocViews Annotation affy

updated 16.6 years ago • Cei Abreu-Goodger

cutoffPre=3,   cutoffFstat=5e-02,   nPermute=20,   seeds=NULL,   writeOutput=FALSE,   lowMemDir=NULL,   smooth=FALSE,   weights=NULL,   smoothFunction=bumphunter...calculatePvalues(coveragePrep = prep, models = models, fstats = fstats, …

derfinder genomicfeatures genomicranges

updated 8.4 years ago • fruce_ki

pattern = ".pos", 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 = "0.99.0", email = "myemail...genomebuild = "HG 18", organism = "Human", species = "Homo sapiens") makePdInfoPackage(seed, destDir = ".") *After the…

BiocViews Annotation Organism biocViews pdInfoBuilder charm BiocViews BiocViews Annotation

updated 13.7 years ago • zeynep özkeserli

geneList_TP_VL, fun="GSEA",TERM2GENE = hallmark_gs, pAdjustMethod="fdr", seed=TRUE, by="fgsea") Fehler in .stopf("Duplicate values in %s not allowed", universeArg) : Duplicate values in names(stats) not allowed

GSEABase

updated 11 months ago • Sidra.Gull

set.seed (9832)` directly inside my package and then I tried to reproduce the results using same seed (see code that follows). Any idea how I could reproduce using the same exact same sampling from `set.seed (9832)` using `clusterSetRNGStream

parallel seed

updated 3.5 years ago • ZheFrench

Where can we find the sample data i.e. "test.expressiondata.txt" used in the TissueEnrich? I tried to run it with my sample data and it showing error as follows: ``` >expressionData<-read.table(data, header=TRUE, row.names=1, sep='\t')Error in read.table(data, header = TRUE, row.names = 1, sep = "\t") : no lines available in input In addition: Warning message: In file(file…

normalization tissue-specific genes TissueEnrich Package

updated 6.7 years ago • hukam.rawal

to run the standard: 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 will be made...use the template below to create your package: ## code to build HTA annot pkg library(pdInfoBuilder) seed <- new("AffyHTAPDInfoPkgSeed", vers…

Annotation oligo pdInfoBuilder Annotation oligo pdInfoBuilder

updated 11.9 years ago • Benilton Carvalho

be used for assing a single value of 'nSigs'?  For decomposition methods with random seeding, values greater than 1 are reasonable. \#==== I understood that values greater than 1 are reasonable but i would like to know

somaticsignatures

updated 10.4 years ago • Asma rabe

fileName = Illumina_8v, metaDataSrc = myMeta,baseMapType = "gb", outputDir = tmpout) seed <- new("AnnDbPkgSeed", Package = "Illumina8vprerelease.db", Version = "1.0.0", PkgTemplate = "HUMANCHIP.DB", AnnObjPrefix = "Illumina8vprerelease...makeAnnDbPkg(seed, file.path(tmpout, "Illumina8vprerelease.sqlite"), dest_dir = tmpout) #### however I fail, when I check the package integrity

Annotation affy AnnotationDbi Annotation affy AnnotationDbi

updated 16.0 years ago • John Lande

I'm trying to run classifySingleR function from SingleR package using MouseRNAseqData() as a reference to classify the cells from a Seurat dataset that has not yet been published, but I got the following error: Error...I'm trying to run classifySingleR function from SingleR package using MouseRNAseqData() as a reference to classify the cells from a Seurat dataset that has not yet been publishe…

SingleR SingleCell

updated 3.4 years ago • amit.korngut

data 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. After typing R CMD check "path/to/my/tarball

BSgenome BSgenome BSgenome BSgenome

updated 13.0 years ago • Sara Castelletti

GRanges())) #> [1] TRUE is.null(dim(DataFrame())) #> [1] FALSE is.null(dim(DelayedArray(seed = matrix()))) #> [1] FALSE is.null(dim(SummarizedExperiment())) #> [1] FALSE ``` <sup>Created on 2020-02-25 by the \[reprex package\](https://reprex.tidyverse.org

class S4

updated 5.9 years ago • Teun van den Brand

just slurps in the entire BAM and then takes a sample: ```r sampleBam <- function(fn,sampleSize,seed) { set.seed(seed) par <- ScanBamParam(what=c("seq","qual","qname"), tag=c("BC","B2"), reverseComplement=TRUE) yield_ <- function(b) { df <- as...to do this would be to read the BAM in chunks: ```r sampleBam…

GenomicFiles ShortRead Rsamtools

updated 4.9 years ago • robmaz77

<div class="preformatted"> Hi, mas5calls function is very usefull for getting p-values and P/M/A calls. I have been wondering about the discrepancy between p-value of R-affy and that of original MAS5. Today I found the reason. R-affy performs Wilcoxon test on (PM-MM) vs tau (default 0.015), on the other hand, MAS5 performs Wilcoxon test on (PM-MM)/(PM+MM) vs tau value. In my case, for e…

updated 22.0 years ago • t-kawai@hhc.eisai.co.jp

website at http://www.affymetrix.co m/analysis/downloads/lf/tiling/Hs35b_PR_v01-3_NCBIv36.bpmap.zip seed <- new( "AffyTilingPDInfoPkgSeed", bpmapFile = bpmap, celFile = celfile, author = "Cindy Yao", biocViews = "AnnotationData", genomebuild...36", organism = "Human", species = "Homo Sapiens" ); # create package makePdInfoPackage(seed, destDir = cfg$pl…

BiocViews Organism biocViews oligo pdInfoBuilder BiocViews BiocViews Organism biocViews

updated 13.8 years ago • Guest User

<div class="preformatted">Dear all, I am looking for differentially expressed genes using multtest package, MTP procedure. I am computing raw and adjusted t-test P values (group 1 = 7 samples, group 2 = 3 samples) using bootstrap. R is running out of memory ('Error: cannot allocate vector') when the number of genes (5413) combined with the number of bootstrap iterations (B=10000) produce a…

genefilter PROcess genefilter PROcess

updated 17.8 years ago • Timur Shtatland

500, pvalueCutoff = "none", pAdjustMethod = "BH", verbose = TRUE, seed = FALSE) go.df <- data.frame(gsepa) go.df <- lsr::sortFrame(go.df, pvalue) GOList <- vector('list', nrow(go.output)) for (i in 1:length

ReactomePA

updated 3.6 years ago • curiousmind007

xys", full.names = TRUE)[1] pos <- list.files(baseDir, pattern = ".pos", full.names = TRU seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, posFile = pos, author = "Name", email = "email", biocViews = "AnnotationData...unspecified", organism = "unspecified", species = "unspecified") makePdInfoPackage(seed, destDir…

microarray R oligo micro array data annotation

updated 10.4 years ago • zenekzkk

I have 20 datasets from different parts and developmental stages of the fruit (seed, flesh fruit, peel). A total of 205,482 genes were retained after filtering genes (with TPM values) with coefficient of variation

WGCNA

updated 4.1 years ago • wes

_I recently encountered an error while trying to estimate mRNA synthesis, processing, and degradation rates using the INSPEcT package. The developer assisted in helping me correct the issue. I've reproduced the error and solution here in case others run into a similar issue._  The [INSPEcT](http://www.bioconductor.org/packages/devel/bioc/html/INSPEcT.html) package estimates mRN…

INSPEcT software error

updated 7.8 years ago • kent.riemondy

how-to-run-permutations-using-mclapply-in-a-reproducible-way-regardless-of-numbe>). There are two easy solutions: (1) Generate the permuted sample indexes before parallel computations. In this way, set.seed() can be used outside...of my R function. (2) Generate a vector of seeds (provided by users through argument of my R function) and use them by set.seed() in each paralle…

BiocParallel

updated 7.0 years ago • luluchen

Hello, I am creating a BSGenome package for Solanum lycopersicum using this seed file and this package is very new to me: Package: BSgenome.Slycopersicum.SGN.SL3.00 Title: Full genome sequences for

BSGenome

updated 6.2 years ago • zen

<div class="preformatted">Hi, Is there a maximum number of sequence files (chromosomes or contigs in my case) that can be fed to the forgeBSgenomeDataPkg() function? I am trying to build a BSgenome for C. brenneri and C. japonica available from EnsemblGenomes. These genomes are made from thousands of contigs with genes annotated to them. Currently, I get the following error when running "E…

BSgenome BSgenome genomes BSgenome BSgenome genomes

updated 12.8 years ago • Marco Blanchette

version of R? I have downloaded the source package and can locate said "Dmelanogaster.UCSC.dm3-seed" I can't seem to work my way through this step. Any suggestions? Thanks in advance. -- output of sessionInfo(): > library(BSgenome.Dmelanogaster.UCSC.dm3

Annotation BSgenome BSgenome DESeq DEXSeq Annotation BSgenome BSgenome DESeq DEXSeq

updated 13.6 years ago • Guest User

fasta = NULL, gtf = NULL, seqpath = NULL, count_random, outdir = ".", paired = TRUE, seed = NULL, ...) ``` Anybody ever tried something similar? Are there tools for simulating reads with differential variance

polyester simulation RNA-seq syntheticdata

updated 5.1 years ago • Endre Sebestyen

I've been using DESeq2 for differential expression analysis of microbial (meta)transcriptomic datasets and have been very happy with its performance. I've started to overlay pathway analyses onto these differential expression results to identify functional groupings of genes (via KEGG or SEED) that are over- or under-represented in these DE gene sets. In parallel, I'd also like to be able to take…

deseq2 pathway analysis order normalization

updated 9.0 years ago • Matt

14 15 > Y <- c(rep(0,nSam), rep(1,nSam)) > print(Y) [1] 0 0 0 0 0 1 1 1 1 1 > > seed <- 99 > for (B in c(100, 1000, 10000, 100000)) { + TTBoot <- MTP(X=X, Y=Y, test = "t.twosamp.unequalvar", alternative = "two.sided", typeone...fdr", method="ss.maxT", fdr.method="conservative", B=B, seed=seed) + MTPRes <- data.frame(PRaw=T…

multtest multtest

updated 17.9 years ago • Timur Shtatland

an error ``` Examining, the object, I can see that `sce_reload@assays@data@listData$counts@seed@filepath` points to the original full path. **Is there are way to save a `SingleCellExperiment` object with a `DelayedArray

HDF5Array SingleCellExperiment DelayedArray

updated 3.3 years ago • merv

5,reps=50, pItem=0.8, pFeature=1, title=title,clusterAlg="hc", distance="pearson", seed=42, plot='png

ConsensusClusterPlus RNASeqData

updated 23 months ago • Diana

but it seems not... I dunno if it has to do with the format I am using to define the seqnames in the seed file which looks like this: *It seems that when posting it the underscores between characters are gone... which make it seem

bsgenome forgebsgenome getSeqSrcpaths

updated 6.8 years ago • tguerreroa90

file.copy(AnnotationHub::cache(ah3["AH91625"]),"./org.Pseudomonas aeruginosa PAO1.eg.sqlite") seed <- new("AnnDbPkgSeed", Package="./org.Pseudomonas aeruginosa PAO1.eg.db", Version="0.0.1", PkgTemplate="NCBIORG.DB",AnnObjPrefix...aeruginoa PAO1") # include your problematic code here with any corresponding output makeAnnDbPkg(seed,"./org.Pseudomonas aeruginosa PAO1.eg.sqlite") Error in …

AnnotationHub AnnotationForge Pseudomonas_aeruginosa

updated 3.1 years ago • Manmohit

file.copy(AnnotationHub::cache(ah3["AH91625"]),"./org.Pseudomonas aeruginosa PAO1.eg.sqlite") seed <- new("AnnDbPkgSeed", Package="./org.Pseudomonas aeruginosa PAO1.eg.db", Version="0.0.1", PkgTemplate="NCBIORG.DB",AnnObjPrefix...PAO1") # include your problematic code here with any corresponding output #makeAnnDbPkg(seed,"./org.Pseudomonas aeruginosa PAO1.eg.sqlite") Error in init…

AnnotationHub AnnotationForge Pseudomonas_aeruginosa

updated 3.1 years ago • Manmohit

TRUE )[1] # take first array tab <- list.files(pathAnnotPr, pattern = "_tab", full.names = TRUE) seed <- new("AffyExpressionPDInfoPkgSeed", cdfFile = cdf, celFile = cel, tabSeqFile = tab, author = "xx", email = "xx", biocViews = "AnnotationData...genomebuild = "hg19", organism = "Human", species = "Homo Sapiens", url = "xx" ) makePdInfoP…

BiocViews Annotation Cancer Organism cdf probe affy biocViews BiocViews BiocViews Cancer

updated 12.6 years ago • Max Kauer

Hello everyone, I have the TMP from RNAseq data. These data come from Arabidopsis seeds infected with a fungal inoculum. Sequencing reads were aligned to the Arabidopsis transcriptome using Salmon, version

Arabidopsis_thaliana removeisoforms WGCNA

updated 2.7 years ago • Ortega-C

group. Cannot calculate variance. This problem may be resolved if you try again with a different seed.</pre> This error remains even after removing all missing (NA) values list-wise.   Any help will be appreciated,  Thanks

multtest methylation adjusted pvalue

updated 10.1 years ago • elhananby

sizeDups=sizeDups, percSNPs=0.1, bpFlankSize=50, repeatBias=TRUE, repeatMaskerFile="hg19.fa.out", seed=223456) and the response I get when running: Calculating coordinates: 100 translocations   |========         &nbsp

RSVSim

updated 10.5 years ago • chimaeran96

I created a directory include two files : maize.2bit (generation by faToTwoBit) maize.seed (seed file) Package: BSgenome.zmv2 Title: Full genome sequences for zea mays ( version 2.0) Description: Full genome sequences

bsgenome

updated 11.0 years ago • qiwang1993

cel <- list.files(path = baseDir, pattern = 'CEL$', full.names = TRUE) stopifnot(length(cel) == 1) seed <- new("AffyTilingPDInfoPkgSeed", bpmapFile = bpmap, celFile = cel, author = "Eric Foss", email = "efoss@fredhutch.org", biocViews...sacCer1", organism = "Yeast", species = "Saccharomyces cerevisiae") makePdInfoPackage(…

oligoClasses oligo pdInfoBuilder

updated 4.5 years ago • efoss

something but the help file for makeAnnDbPkg() has the following example: > makeAnnDbPkg(seed, "path/to/hgu133a2.sqlite") Looking at the source code of makeAnnDbPkg() I get: setMethod("makeAnnDbPkg", "character", function

AnnotationDbi AnnotationDbi

updated 15.5 years ago • cstrato

more details about the problems you are having? (Any error message you get, the content of your seed file, your sessionInfo(), etc... anything that could help us diagnose the problem). Also have you tried to forge a small BSgenome

Cancer BSgenome BSgenome Cancer BSgenome BSgenome

updated 16.5 years ago • Hervé Pagès

I need help in making sure my model is correct for my experiment and that I am running the analysis correct using the LRT for timecourse data with Deseq2 in R. I am trying to run a differential gene expression analysis with RNAseq data for seeds from multiple years (3) and imbibed over multiple timepoints (3). I have tried using the LRT example and wanted to check if...with Deseq2 in R. I am …

RNAseqRData DeSeq2

updated 3.8 years ago • ANNA