Bioconductor Forum

PACKAGE = > "IRanges") : In range 2160: at least two out of 'start', 'end', and > 'width', must be supplied. > 6. .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges"). > 5. solveUserSEW0(start = start, end = end, width...width). > 4. IRanges(peaks[, 2], width = peaks[, 3] - peaks[, 2] + 1, names = rownames(peaks)). > 3. G…

DiffBind

updated 4.6 years ago • Bei Jun

dat_filtered, coldata, design=~batch+cell_num+group) converting counts to integer mode factor levels were dropped which had no samples Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model...variables or interaction terms in the design formula are linear combinations of the others and must be removed. Please read the vignette section 'Model matrix no…

DESeq2 DEs

updated 21 months ago • feather-W

binding. Limma uses the median of the background because (i) here the aim is to measure the ambient level, not the total binding, and (ii) because it is desirable for noise reduction for the background to be slightly lower than...distribution is lower than the mean. > Would the assumption here be that the spot morphology > must be impeccable? I have not yet seen any compelling ev…

limma limma

updated 20.8 years ago • Gordon Smyth

pData(eset) > targets<-pData(eset) > model.matrix(~ -1 +factor(targets$Target,levels=unique(targets$Target))) > design <- model.matrix(~ -1 + > factor(targets$Target,levels=unique(targets$Target))) > unique...lt;- colnames(design) > design > fit <- lmFit(eset,design=design) > name…

updated 19.5 years ago • Gordon Smyth

I have received from this forum). My follow-up question is as follows : Depending on the threshold level chosen to create a binary image, the percent area calculated will vary. I would like to have a means of visualizing the...uncertain regions represented by a threshold band level on the original image. If we start with the following code : library(CRImage) img = readImage(system.file("images", …

PROcess PROcess

updated 13.3 years ago • Guest User

the commands I used: > > conditions = c( "HCV1", "HCV1", "HCV1", "HCM1", "HCM1", "HCM1" ) > names(conditions) <- c( "accepted_hits_ATCACG.sorted.bam", "accepted_hits_CGATGT.sorted.bam", "accepted_hits_TTAGGC.sorted.bam...I got an error: > Error in match.arg(trend, c("none", "movingave", "tricube")) : > 'arg' must be NULL or a character vector > &…

Organism edgeR easyRNASeq Organism edgeR easyRNASeq

updated 13.3 years ago • delhomme@embl.de

Cloud AMI. Today I started to use it again. But I was failed and got this message: Error Template validation error: Parameter InstanceType failed to satisfy constraint: Choose a valid EC2 instance type from http://aws.amazon.com

updated 11.6 years ago • Rohmatul Fajriyah

Hello! I am trying to analyse the differential gene expression between groups in a complicated multi-factor experiment and am having trouble setting up the contrast matrix. In this experiment, samples were collected from three different geographic origins (Brazil, California and Yemen), were kept under one of four different regimes (ancestral, hot, cold, switch), and RNA was assayed at one of th…

edgeR

updated 2.2 years ago • alex.hart

function of sva package. My expression matrix like this，the row is gene ID, the col is sample name; <table style="height:114px; width:288px"> <tbody> <tr> <td>Gene ID</td> <td>FPKM_SRR1747143</td> <td>FPKM_SRR1747144</td> <td>FPKM_SRR1747145...FLASE) But I got a wrong message : Found3batches Adjusting for0covariate(s) or …

sva combat

updated 7.4 years ago • linw

variables (Var1, Var2, Var3, Var4). My code is as following: ``` #(1) TukeyHSD test vars <- names(df)[-1] aov.out <- lapply(vars, function(x) { lm(substitute(i ~ technique, list(i = as.name(x))), data = df) }) ## only get adjusted p-value (according

StatisticalMethod

updated 3.7 years ago • dong

Dear developer & users, Hi, I've been trying GreyListChIP but was not succeed when using own bam file (The package installation is alright, which tested by the sample data) Here's the code: <pre> library(GreyListChIP) library(BSgenome.Mmusculus.UCSC.mm10) path <- system.file("extra", package="GreyListChIP") fn <- file.path(path,"T1-D0-I.dup.removed.sort.bam") g…

GreyListChIP

updated 8.1 years ago • kyliecode

help, Francesco > novel.data<-as.data.frame(novel.snps) > novel.data<-cbind(novel.data,name=row.names(novel.data)) > head(novel.data) seqnames start end width strand ALT name chr22:17468875 chr22 17468875 17468875...gt; targetTrack <- with(novel.data, + GRangesForUCSCGenome("hg19",seqnames,targetRanges,strand,name)) > ses…

SNP BSgenome BSgenome rtracklayer SNP BSgenome BSgenome rtracklayer

updated 13.9 years ago • Lescai, Francesco

R for DeSeq2 analysis but I can't seem to get the first column of my colData to match the column names of my countData. The match (vector 1, vector 2) function isn't working and I think it has to do with the layout of my data. The

deseq2 bioconductor

updated 6.8 years ago • ishtarredman

trt** followed by ashr fold-change shrinkage. I get different results with ashr with reference levels compared to the ones without defining the reference levels (**see above table for example**). - My question is "How is it possible...1, sep="\t") edf = read.table("edf.txt", row.names = 1, header=1, sep="\t") # with reference levels dds <- DESeqDataSetFromMatrix(countData = ma…

DESeq2 RNASeq

updated 4.6 years ago • sofiagreen72211

and drug sensitivities / resistances in tumours • Development of experimental platforms to proof / validate mechanistic insights Work on these tasks will be shared with a focus on statistical method development and theoretical...Qualifications and Experience The positions are highly inter-disciplinary. P1 requires PhD-level expertise in statistics, physics, computer science, bioinformatics, …

exciting Job

updated 10.5 years ago • Wolfgang Huber

rank][1] describes, my data have variable(s) that can be formed by the combination of other factor levels. For this reason running: ``` DESeq2::DESeqDataSetFromMatrix(countData = count.mat, colData = df, design =~ cov1 + cov2 + animal_id...variables or interaction terms in the design formula are linear combinations of the others and must be removed. Please read the vignette section …

DESeq2 paired design

updated 4.3 years ago • dr

problem GOIDs from topGO are GO:0030522, GO:0051094, GO:0031497, GO:0046700. I can't find these in names(Mm.egGO2EG). library("org.Mm.eg.db") Mm.egGO2EG <- as.list(org.Mm.egGO2EG) grep("GO:0030522",names(Mm.egGO2EG)) integer...using org.Mm.eg.db? When I check for GO:0030522 for Mus musculus at geneontology.org, GO:0030522 is valid. I'm puzzled by the mismatch. I want to get the genes …

GO Mus musculus PROcess topGO GO Mus musculus PROcess topGO

updated 15.8 years ago • Dick Beyer

[**Click here to learn more and apply online**][1] **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…

Bioinformatics research seattle Job

updated 6.2 years ago • Fred Hutch (Recruiting)

datasetconfigversion="0.6" requestid="biomaRt" uniquerows="1" virtualschemaname="default"> <dataset name="hsapiens_gene_ensembl"><attribute name="affy_hg_u95av2"></attribute><attribute name="hgnc_symbol"></attribute><filter name...research assistant www.dcs.gla.ac.uk/~lisa/<http: %7elisa="" www.dcs.gla.ac.uk=""></http:> R315 Level 3 Paul O'Gorman L…

biomaRt biomaRt

updated 13.8 years ago • Lisa Hopcroft

functions, 2 errors, 0 failures ERROR in test_AtomicList_general: Error in match.arg(method) : 'arg' must be of length 1 ERROR in test_AtomicList_numerical: Error in match.arg(method) : 'arg' must be of length 1 VariantAnnotation...80 test functions, 1 error, 0 failures ERROR in test_VRanges_vcf: Error in match.arg(method) : 'arg' must be of length 1</pre> Any suggestions on how to t…

biocgenerics iranges variantannotation

updated 8.2 years ago • ginggs

function to accept a user provided common dispersion value, but I am not sure this is entirely valid. The question being how to populate the pseudo.alt slot when you are estimating the common dispersion parameter yourself...and whether it is even valid to do so. Cheers Mick -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number

updated 13.1 years ago • WATSON Mick

58294): ENSG00000000003.14 ENSG00000000005.5 ... ENSG00000285993.1 ENSG00000285994.1 rowData names(1): gene_id colnames(8): SRR1039508 SRR1039509 ... SRR1039520 SRR1039521 colData names(3): names donor condition ``` 2) rename...gt; (gse$cell <- gse$donor) [1] N61311 N61311 N052611 N052611 N080611 N080611 N061011 N061011 Levels: N052611 N061011 N080611 N61311 > (gse$dex &lt…

DifferentialExpression GeneExpression DESeq2 Design()

updated 4.2 years ago • p.l.chen

highest beta (_"equivalent"_ to log fold change) were around 6 and the lowest -4. In order to validate my results from Sleuth, I wanted to use __DESeq2__ to see if I got similar results (+ make _"prettier"/customizable_...Kallisto-data files <- file.path(dir,"results", samples$path, "abundance.tsv") names(files)<- paste0(samples$Sample)…

deseq2 tximport rnaseq kallisto R

updated 8.5 years ago • birgittenilsson

not allowed non-unique values when setting 'row.names':  But I know for sure that my row names are unique!  Any advice would be appreciated. Thanx. carol

edgeR row.names DGEList

updated 10.8 years ago • ccheung

I use the library`` EnsDb.Mmusculus.v79 ``. However, I am somehow not able to retrieve the gene name (description). Based on the retrievable annotation info, I assumed this would be accessible through the argument`` columns

EnsDb.Mmusculus.v79 ensembldb annotation

updated 8.3 years ago • Guido Hooiveld

dataset = dataset, mart = mart) : The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. mart <- useEnsembl(biomart = "ensembl",dataset

biomaRt

updated 10 months ago • rayanelkholdi

Sample") files <- file.path("first_batch/first_batch_salmon_trinity_full/", dirs, "quant.sf") names(files) <- dirs ######### gene level tx2gene <- read_delim(file.path("first_batch/first_batch_salmon_trinity_full/", "Trinity.fasta.gene_trans_map...col_names = FALSE) %>% dplyr::select(X2, X1) names(tx2gene) <- c("tr…

DESeq2

updated 21 months ago • Emma

not really need to know about the classes -> they should be relatively transparent at the user level. " In order to do anything not written into Bioconductor, I needed to understand the classes. The documentation is good...m[1,4]). Many R functions return objects which are lists. Components of a list can be extracted by name (list$mydata) or by component number (list[[3]]). Anythin…

updated 21.7 years ago • Naomi Altman

In read.table(file = file, header = header, sep = sep, quote = quote, : not all columns named in 'colClasses' exist > sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu

GEOquery

updated 9.6 years ago • alexvpickering

After that i make my contrasts: > makeContrasts(subject1,subject2,subject3,subject4, levels = design) Contrasts Levels subject1 subject2 subject3 subject4 subject1 1 0 0 0 subject2 0 1 0 0 subject3 0 0 1 0 subject4...library( reshape ); library( FactoMineR ); analyse <- functio…

edgeR edgeR

updated 11.3 years ago • Guest User

end) > targetTrack <- with(targets,GRangesForUCSCGenome("hg18", chrom, targetRanges, strand,name, target)) > session <- browserSession("UCSC") > track(session, "targets") <- targetTrack Fehler in genome(seqinfo(x)) : Fehler...f??r Funktion 'genome': Fehler in .normargSeqlengths(seqlengths, seqnames) : supplied 'seqlengths' must be a vector R version …

rtracklayer rtracklayer

updated 13.9 years ago • Guest User

done Processing flanking windows in Chr4 <strong>Error in FUN(X[[i]], ...) : assay rownames() must be NULL or equal rowData rownames() / rowRanges names()</strong></em></pre>   &nbsp

soGGi chip-seq region

updated 8.3 years ago • 835102330

fisher",verbose=F) Error in spia(de = WThypo, all = WThypo1, organism = "mmu", nB = 2000, : de must be a vector of log2 fold changes. The names of de should be included in the refference array! I am not sure what I did wrong

Organism SPIA Organism SPIA

updated 14.3 years ago • Jing Huang

value)))){ # The columns I don't want overwritten/removed all begin with "pos" stop("Column names of user-specified 'mcols' must not begin with 'pos'") } GenomicRanges:::clone(x, rowData = local({ r <- rowData(x) mcols(r) <- cbind(mcols

GenomicRanges GenomicRanges

updated 11.7 years ago • Peter Hickey

called ctc and cluster. On the SMD website, I downloaded Xcluster for windows. In R, I write : name<-xcluster(file) R wrote : Xcluster isn't install I don't know what I must do to cluster my data. Someone can help me Thanks [[alternative

Microarray ctc Microarray ctc

updated 20.4 years ago • Antoine Lucas

<div class="preformatted">I have a simple loop of 2-color cDNA microarray experiments containing 6 individuals and 2 technical replicates for each. After batch and printtip normalization I need the intensity values for each feature, for each individual. I ran the following script using lmFit to obtain coefficients for each feature, for each individual: > design <- modelMatrix(…

Microarray Normalization Microarray Normalization

updated 17.4 years ago • Lin Huffman

I would like to take the results of a BLAST search and look at their location on a de novo genome. I'm running into an issue creating the GRanges object and I believe this is because many of the BLAST results hit to the same scaffold.  As I understand it, GRanges requires a seqname for each row of data (where each row corresponds to one line of tabular blastn output). I would like to ad…

GRanges seqnames seqlengths IRanges

updated 11.2 years ago • topher.hamm

TP1.WTvs.T = T1.T - T1.WT, TP2.WTvs.T = T2.T - T2.WT, TP3.WTvs.T = T3.T - T3.WT, levels=design) glmQLFTest(fit, contrast = TP1.WTvs.T) # single TP comparison glmQLFTest(fit, contrast = con) # compare all time points...strainT.timeTP1" ## [9] "strainT.timeTP2" ... By calling **`results(dds, name="time_TP2_vs_TP0")`** I can detect all genes in WT w…

deseq2 time-series design matrix edger

updated 6.8 years ago • Assa Yeroslaviz

status was `404 Not Found' Note: http://www.bioconductor.org/CRANrepository does not seem to have a valid repository, skipping Warning message: Failed to read replisting at http://www.bioconductor.org/CRANrepository in...3.4.2/../../.. -lfrtbegin -lg2c -lSystem -lcc_dynamic -framework R ld: warning -L: directory name (/usr/local/lib) does not exist ld: warning -L: directory name (/usr/local/lib) …

Microarray genefilter multtest Microarray genefilter multtest

updated 20.8 years ago • Monnie McGee

catabolic process" has 218 terms in the original but it has 313 terms in the new result ??? This must be due to ENSEMBL database because they both have the same input data files. Anyone has any advice/suggestion?   &nbsp...nbsp;   genelist<-factor(as.integer(geneuniverse %in% geneofinterest))     names(genelist)<-geneuniverse &nbsp…

R ENSEMBL topGO

updated 8.0 years ago • snguyen268

27998): ENSMUSG00000051951 ENSMUSG00000089699 ... ENSMUSG00000096730 ENSMUSG00000095742 rowData names(2): id symbol colnames: NULL colData names(2): dataset barcode reducedDimNames(0): spikeNames(0):</pre> and I would like to use...log2( + calculateCPM(sce10x, use.size.factors = FALSE) + 1) Error in colSums(counts_mat) : 'x' must be an array of at least two dimensions</pre&g…

scater SingleCellExperiment

updated 8.2 years ago • chriad

Hi, I'm having some troubles trying to filter a SingleCellLoomExperiment object by its colData. I made a subset with 100 columns , an I want to filter by the variable Tissue in colData to be equal than "DRG". Does anyone know what I'm doing wrong? Many thanks! ``` > scle.all class: SingleCellLoomExperiment dim: 27998 100 metadata(0): assays(2): matrix logcounts rownames(…

SingleCellLoomExperiment

updated 5.6 years ago • marc.tormo

with SYMBOL... Error: 2 errors; first error: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL' For more information, use bplasterror(). To resume calculation, re-call

Annotation Preprocessing hgu133plus2 hgug4112a

updated 11.3 years ago • Guest User

not using 4 separate symbols, each with its own color. Instead, I want use 2 symbols to indicate the levels of the first factor and 2 colors to indicate the levels of the second factor. I can do this by using the arguments "pch" and...length(gps); if you forget to put in groupnames in the original call to plotPCA, it defaults to the names of the columns, and the legend symbols get recycled so tha…

updated 18.9 years ago • Jenny Drnevich

lt;- factor(x$UCSC) library(RColorBrewer) mycol <- brewer.pal(6, "Set1") ## if you only have 6 levels heatmap.2(z.ma, ..., RowSideColors=mycol[f]) The legend can be recreated by legend(x="topleft", legend=levels(f), col=mycol[factor...levels(f))], pch=15) If you want to superimpose the legend on the plot generated by heatmap.2(), you will need to adjust the x, y argument...RowSideColor…

Cancer convert Cancer convert

updated 14.1 years ago • Chao-Jen Wong

<div class="preformatted"> I'm having trouble reading in my raw cel files and am unable to interpret the error message. Please see my error and code below. Last time I had to add varmetadata() info. and it worked, but that doesn't see to help in this case. Any suggestions will be appreciated. Thanks. Error: > OligoRaw = read.celfiles(filenames=list.celfiles(),phenoData=pd, verbose…

affy oligo arrayQualityMetrics a4 affy oligo arrayQualityMetrics a4

updated 11.9 years ago • Guest User

<div class="preformatted">In an experiment with 3 or more conditions (treatments, levels ...) it is usually necessary to have more contrasts than can be accommodated by the design matrix. That is why there is fit.contrast as well as lmFit. My approach is to loop designs is to use single channel analysis. It is simplest to pick an arbitrary condition as the reference for the design matrix,…

limma limma

updated 20.0 years ago • Naomi Altman

3), rep("kd_cpt",3) ) samples = as.factor(samples) design=model.matrix(~0 + samples) colnames(design) = levels(samples) fit = lmFit(exprs(BSData.filt), design) cont.matrix=makeContrasts(diff_con=con_veh - con_cpt, diff_kd=kd_veh...kd_cpt, levels=design) fit=contrasts.fit(fit, cont.matrix) fit$genes=fData(BSData.filt) ebFit=eBayes(fit) library(illuminaHumanv3.db...as.character(ids), Chr = as.char…

GO GO

updated 15.1 years ago • Moritz Kebschull

pre> Obviously this interfers with annotation so have split it by + and annotated both for gene names etc. However with many of them per dataset I wondered how best to handle them quickly and easily? I know I could manually

rnaseq deseq2 ensembl

updated 8.6 years ago • Nicholas Owen

hgnc_symbol[ idx ]</pre>   I'd now like to use this on a dataframe where the input row names are transcript IDs (e.g. ENST000...). I'm not sure whether I can do this with BioMart - does anyone know

rnaseq r biomart

updated 10.0 years ago • kmuench

test.h5") h5createDataset(file="test.h5", dataset="A", dims=c(20000,10000), chunk = c(20000,10), level=3) for (i in 1:1000) { print(i) S = matrix(rnorm(200000), nrow=20000, ncol=10) h5write(obj=S, file="test.h5", name="A", index=list(NULL,1:10+(i-1...a minute to fill the dataset with random numbers. You can now even use compression, e.g. by setting level=3. This increases the runtime to fi…

rhdf5 rhdf5

updated 11.7 years ago • Bernd Fischer

cdffile.path="C:\\Users\\EKL\\Downloads\\GPL8345_AFLAVUSa520391F.cdf") Error: the following are not valid files: C:\Users\EKL\Downloads\GPL8345_AFLAVUSa520391F.cdf > eset<-ReadAffy(cdffile.path="C:\Users\EKL\Downloads...cdffile.path="C:\\Users\\EKL\\Downloads\\GPL8345_AFLAVUSa520391F.cdf") Error: the following are not valid files: C:\Users\EKL\Downloads\GPL8345_AFLAVUSa…

affy CDF

updated 6.1 years ago • ekl

Reg: makePdInfoPackage Error in sqliteExecStatement(con, > >statement, bind.data) : bind.data must have non-zero dimensions > > > >Hi Nitesh, > > > > > >can you please "re-read" the ndf? use: > > > >ndf = read.table...makePdInfoPackage Error in sqliteExecStatement(con, > >…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.3 years ago • Benilton Carvalho

__Summary:__ The Center for Biomedical Informatics (CBMI) [https://cbmi.med.harvard.edu](https://cbmi.med.harvard.edu/) at Harvard Medical School is looking for a Research Associate to help build cutting edge research platforms. The real value in biomedical research lies not in the scale of any single source of data, but in the ability to integrate and interrogate multiple, complementary dataset…

reseach phenotype extraction biomedical ontologies Job

updated 11.1 years ago • Doe, Aimee

it comes down to setting the environment variable http_proxy to your proxy server (note that it must be set before starting R). If your proxy server requires a user name and password you may also have to set http_proxy_user...use the form "ftp://proxy.dom.com:3128/" where the default port is 21. These environment variables must be set before the download code is first used: they cannot be altered…

Microarray Microarray

updated 21.5 years ago • Christopher Wilkinson

lt;-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, ... : duplicated levels in factors are deprecated 6: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, ... : duplicated levels...in factors are deprecated 7: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, ... : duplica…

R riboseqr ribosome profiling

updated 10.1 years ago • ohtack9

a qDE.limma file for subsequent analysis and visual representation. Strangely, I lose my gene names after running the limmaCtData function. Am I doing something wrong? <pre> raw <- readCtData(files = "1131361180.csv", path...An object of class "qPCRset" Size: 48 features, 18 samples Feature types: Feature names: PD1 BCL6 BATF ... Feature classes: F…

limma htqpcr

updated 10.3 years ago • julio.c.silver

I don???t know if it is a problem): - I searched for semicolons and single quotes ??? in the gene names, but I didn???t find any on the final file. - I deleted all the columns after gene_name. So finally the annotation file entries...Ggallus", chrSizes = "chrSizes", : Your organism has no mapping defined to perform the validity check for the UCSC compliance of the chromosome name. Defined o…

Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq

updated 12.1 years ago • Guest User

for my analysis. I have two files for the data: one is an Excel file (including time points and the names of the samples, such as "stimulated vs. non-stimulated" controls), and a text file containing gene expression data (RNA-seq...library (DESeq2) coldata <- data.frame(row.names = colnames(GeneMat), condition) #check if col names = row names ## must say TRUE all(rownames(coldata) == c…

DESeq2 ctsGE

updated 20 months ago • Emma

header = TRUE, row.names=1) > genelist_topGO_5d_1d_all <- as.numeric(gene.table$p.value) > names(genelist_topGO_5d_1d_all) <- as.character(row.names(gene.table)) #My geneList looks good, just like the example, e.g...November/020045.html) > genelist_topGO_5d_1d_all_2 <- as.character(gene.table$p.value) > names(genelist_topGO_5d_1d_all_2) <-…

Microarray topGO Microarray topGO

updated 14.1 years ago • oystercow