Bioconductor Forum

<div class="preformatted">Dear List, I'm starting to do limma analyses on a small timecourse loop design with 2-color cDNA chips as follows: 0h vs 6h 6h vs 24h 24h vs 0h Four biological replicates -> and then four biological replicates dye balanced <- My targets file begins like this (only the first two sets of three listed): US22502600_F82_S0…

TimeCourse limma timecourse TimeCourse limma timecourse

updated 17.9 years ago • Yannick Wurm

Dear Maintainer, I'm analyzing an expression matrix using a single factor with only two levels, 0 and 1. I would like to add in a more than two factor variables from the experiment which measured percent disease progression...then have TIMEPOINT/ %DISEASEPROGRESSIONRATE/OBSERVATIONPOINT/... However, it's just as simple to name each array in TARGETS as "X.timepoint.%DPR.OP", keeping the matrix t…

limma limma

updated 12.4 years ago • Guest User

c("Control","Salt300") gse.expFilt <- varFilter(gse) fit <- lmFit(exprs(gse.expFilt), design) names(fit) dim(fit$coefficients) head(fit$coefficients) contrasts <- makeContrasts(logFC = Salt300 - Control, levels=design) fit2...decideTests(fit2)) sum(abs(decideTests(fit2))==1) volcanoplot(fit2) volcanoplot(fit2,highlight=10,names = fit2$genes$"Symbol") write.fit(fit2…

limma microarray

updated 6.1 years ago • sagayanilo

7-14.txt") d<-read.table("expressionDataHFNIH5-7-14.txt", header=T, row.names=1) names(d)<-gsub(".CEL", "", gsub("X", "", names(d))) d<-round(d, 5) write.table(d, file="filepath.txt", quote=F, sep='\t') #create a design matrix #congestion...1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2)) ID<-factor(design[,1]) Congestion<-factor(design[,2], levels=c("1","…

logFC limma

updated 10.0 years ago • pt2395

Hello, I'm attempting to use the GOstats package to do a differential KEGG pathway analysis in wheat (non-model organism without an organism package). I'm following the guidelines from GOstats for unsupported organisms [here][1]. The problem is at step 1.3, using KEGGFrame in a KeggID/GeneID data frame, where the function returns a message saying the KEGG Ids are not valid. The problem also occ…

AnnotationDbi GOstats

updated 13 months ago • a1869161

45, # of eval=FALSE: 9 (20%) * Checking version number... Checking version number validity... Package version 0.99.0; pre-release * Checking R Version dependency... * Checking package size... * ERROR: Package Source...biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recomm…

package development

updated 7.2 years ago • ntueeb05howard

S4Vectors::Rle(c("chr1", "chr2"), c(2, 1)), IRanges::IRanges(c(1, 4, 2), width=c(4, 8, 6), names=head(letters, 3)), S4Vectors::Rle(GenomicRanges::strand(c("-", "+", "-")), c(1, 1, 1)) ) -> gr (v <- IRanges::Views(cvg, gr)) ``` ``` RleViewsList object of length...expression has 2 elements: only the first used $chr1 [1] (0.997,2] (0.997,2] (2,3] (3,4] Levels:…

Views IRanges GRanges RleList

updated 4.2 years ago • Assa Yeroslaviz

temp files : . || || Threads : 8 || || Level : meta-feature level || || Paired-end : no || || Multimapping reads : counted …

Rsubread

updated 5.6 years ago • kathleen.e.grogan

make a data frame with that)? Thanks Below is my session info. ``` > BiocManager::valid() [1] TRUE > BiocManager::version() [1] ‘3.10’ > BiocManager::valid() [1] TRUE > sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64

software error keggLink R

updated 5.9 years ago • superdanny68

nbsp;                          names<br/> [1] 1962640 CTAACTTGACACCTTTCCCTTG...TCATTCCCCTTCCCACACACAC 1.Genome2<br/> [2] 1962640 CTAACTTGACACCTTTCCCTTG...row index = 2 and so on): <pre> A DNAStringSet instance of length 1674 width seq …

decipher

updated 7.9 years ago • Vinicius Henrique da Silva

Counts from nf-core/rnasplice:** - salmon.merged.transcript_counts.tsv: Matrix of isoform-level raw counts across all samples. - salmon.merged.transcript_counts_scaled.tsv: Matrix of isoform-level scaled raw...level dtu scaled raw counts across all samples. **TPMs from nf-core/rnasplice:** - salmon.merged.transcript_tpm.tsv: Matrix of...isoform-level TPM values across all samples. - salmon…

limma isoform edgeR salmon R

updated 12 months ago • mohammedtoufiq91

says Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments. but the rownames are the ensembl ids!! idfound

edgeR ENEMBL RefSeq

updated 6.7 years ago • mzillur

formula with some parameter that I want to minimise with some condition like sum of all of them must be one, in some condition, one of them must equal 0, etc. I am trying to solve that with constrOptim but I got some broblem... Like

updated 13.8 years ago • SimonNoël

I was just wondering if it's valid to perform SC3 clustering on latent variable normalised counts obtained for example from RUVSeq's RUVg or similar

SC3 single cell

updated 9.1 years ago • Mark

had much success with 'R' but I am open to any suggestions :) I have two text files containing gene name lists;preferably, I want to be able to simply paste these text files and then have a Venn diagram appear. Does such an online

Venndiagram files text

updated 2.9 years ago • ratto

and the identification of novel therapeutic targets. To be considered for this position, you must: - have a PhD in genetics or a closely related discipline - have a high level of programming skills and experience applying...application form. Informal enquiries can be made to Naomi Clark, Metabolic Research Laboratories, Level 4, Well-come Trust-MRC Institute of Metabolic Science, Box 289 Addenb…

genetics job genomics postdoc obesity Job

updated 8.8 years ago • njc65

I want to compute the TMM for two RNASeq-samples in two different conditions. The number of DE genes is different in each sample. In order to compute the TMM normalization is required that the samples have the same genes listed in the corresponding order? If it is the case, how I can do this arrangement? Thanks so much.

TMM edgeR

updated 9.5 years ago • humberto_munoz

to restore these packages. Bioconductor version: 3.18 Error in renv_snapshot_validate_report(valid, prompt, force) : aborting snapshot due to pre-flight validation failure Calls: <anonymous> ... snapshotRenvDependencies...renv::snapshot(bundleDir, packages = deps$Package, prompt = FALSE) 2: renv_snapshot_validate_report(valid, prompt, force) 1: stop("aborting snapshot due to pre-…

BiocVersion phangorn ShinyApps

updated 2.1 years ago • susan

design,weights=NULL)/ cont.matrix=makeContrasts(pollutedVScontrol=polluted- control,polluted,control,levels=design) cont.matrix fit2=contrasts.fit(fit,cont.matrix) fit2=eBayes(fit2) res=toptable(coef=1,number=15744,fit=fit2...one "control array" versus one "treated array". So is it possible to specify to lmFit that there must be a minimum of "1" weights or a maximum "0" weights per groups of arra…

limma limma

updated 16.4 years ago • Benoit

I am getting an error while mapping the gene names to the StringDB identifiers using the map function. The code was working fine before with the StringDB version 11 but

PPI STRINGdb

updated 4.3 years ago • Ashish Jain

hugo) hugo2 <- as.list(hugo[mapped]) hugoDF <- data.frame(PROBE_ID = as.character(names(hugo2)), SYMBOL = as.character(hugo2))</pre> And the same for  other entries, with later merging them like this: <pre> expressionAnnotationData

probe to gene id illumina beadchip probe quality

updated 9.6 years ago • smt8n

NA'-values for the p-values > scores <- log(pmax(last.out at p.value)) > valids <- !is.na(scores) > scores <- scores[valids] > data <- last.data[valids,] I have a list of data (18 Columns x 19,302 rows) I then

convert convert

updated 20.1 years ago • Assa Yeroslaviz

I have a kalliso-created abundance.h5 file but the filename (ES\_1\_high\_28881\_CGATGT\_abundance.h5) includes information about the sample. When I try to import this file using tximport v1.10.0 I get an error. tximport thinks that the file is a .tsv file.  However, if I create a symlink named abundance.h5, I can load that perfectly well.  Is there a way to tell&…

tximport kallisto

updated 6.9 years ago • Lucas Carey

Apply at: http://jobs.jnj.com/job/Spring-House-Janssen-Post-Doctoral-Fellows%2C-Computational-Biology-Job-PA-19477/241331600/ __Description__ Janssen Research and Development, L.L.C., a member of Johnson and Johnson's Family of Companies, is recruiting for Post-Doctoral Fellows, Computational Biology with an emphasis in Immune-Oncology in Springhouse, PA. Janssen discovers a…

Job

updated 10.9 years ago • Michael Gormley

Hello, I was seeking a tutor that could help me with a R course - this is no longer needed, thanks everyone!

bioconductor ALL R Job

updated 7.3 years ago • detroit.drive

a microarray study which was deposited on GEO. I am using the `oligo` package to obtain gene level summaries after background correction. Now I want to map all the remaining probesets to to entrez gene ids, but I wasn...2372103", ...` I would very much appreciated if somebody could tell me what the correct `field` name is to get the gene identifiers, or any other way how I can get gene ids …

AnnotationDbi Microarray

updated 3.6 years ago • nhaus

sample", "dpi14tocv", "dpi14bemisia") >results<-results(dds,contrast = contrast) ``` The name provided in the second element ("dpi14bemisia") is the level that is used as baseline, right? The I added thresholds: ``` ### Set thresholds

deseq2 contrast DEG

updated 6.1 years ago • ire.ontiveros

error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CustomConsensusClusters > ### Title: Expression levels of consensus cluster > ### Aliases: CustomConsensusClusters &gt

biocparallel build report

updated 7.9 years ago • Charles Plessy

<div class="preformatted">hi, while i was using the gene-centric organism-level package for yeast org.Sc.sgd.db i encountered the following error: library(org.Sc.sgd.db) select(org.Sc.sgd.db, cols="ORF", keys=keys(org.Sc.sgd.db, keytype="GENENAME"), keytype="GENENAME") Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near "IMP3": syntax err…

updated 12.5 years ago • Robert Castelo

Hello! I am working on a project where I have a fully-crossed two-factor design, with two levels per factor and four biological replicates per treatment combination (16 biological replicates total across 4 total...in the DESeq function (`data <- DESeq(dds)`). Then running `resultsNames(data)` gets me the names of "Intercept", "RearingTemp_30_vs_16", "TestingTemp_30_vs_16", and "RearingT…

DESeq2 RNASeqData deseq2 ExperimentalDesign

updated 2.1 years ago • Sam

Hi all, Despite reading the DESeq2 vignette (and other useful references), I'm still a little uncertain about how to best test for differential expression in the presence of a group by condition interaction. I have two conditions (for simplicity here cond1 and cond2), and eight species (for simplicity here species1, species2, ..., species8). What I hope to do is look for genes that are differe…

DESeq2 interaction differential expression

updated 5.4 years ago • charles.foster

Dear All, I have a matrix "U2" with 44 samples (41 Disease + 3 Normal) as columns and approx. 15k genes as rows. "coldata" is where samples as rows and columns "Subtypes" and  "Type". Column "Type" is with Disease and Normal. <pre> library(DESeq2) dds <- DESeqDataSetFromMatrix(countData = U2, colData = coldata, design = ~ Type) dds class: DESeqDataSet dim: 15754 44…

deseq2 rnaseq differential gene expression edger

updated 7.5 years ago • Biologist

change for comparison for such two genes was -13.4 and 2.47. Since the 'condition' has more than 3 levels I set the betaPrior to False as Michael indicated in the earlier correspondence (the code appears below). Can you tell...c("U_V0","U_K1", "U_p5","M_V0","M_K1","M_p5") colData$condition = factor( colData$condition, levels = conditionsList) dds <- DESeqDataSetFromMatrix(countData = cou…

Regression DESeq DESeq2 Regression DESeq DESeq2

updated 11.8 years ago • Noa Henig

preformatted">Hello, I have a dataframe df1 and a grange object gr. The rownames respectively names (gr) are identical but not necessary in the same order. I wish to append df1 as metadata to the gr (of course rownames (df) and...names (gr) must fit). Could you please give me a hint. Thanks Hermann > df1 Strand A1 A2 rs3737728 u C T rs6687776 u C T rs9651273 …

updated 12.4 years ago • Hermann Norpois

2014 at 8:10 AM, Noa Henig <ntzunz@gmail.com> wrote: > > Hi Mike, > I was looking at the leveling as you extracted it and I might have done a mistake with the naming of the sample (I'm checking it now), I apologize. > Regarding...the column data, even if it is > not for public viewing, by "scrubbing" the sample and factor level names. > (Note though…

GO DESeq2 GO DESeq2

updated 11.9 years ago • Michael Love

<div class="preformatted">I am using siggenes to do a two class paired analysis of 36 microarrays. I do not appear to have any problems but upon summarizing the results I receive "NA" for fold change. I believe I read somewhere in the vingette that fold change is only calculated for two class unpaired analysis. Is this true? If not, what must I do in order to calculate the fold change i…

siggenes siggenes

updated 17.4 years ago • Mary Winn

color experiment with an Agilent chip. I read the limma User Guide and find out that I must preprocess with the function normalizeBetweenArrays. So I get M- and A-values and my question is which one shows the expression...on the chip Affymetrix Mouse Genome 430 2.0 Array the ID 1449880_s_at stands for three gene names and entrez ids:Bglap /// Bglap2 /// Bglap3 - 120…

RankProd RankProd

updated 11.6 years ago • Stefanie Busch

or physics. A solid foundation in data analysis and programming in a Unix/Linux environment is a must. Knowledge of basic biology is an asset, but is not required. We invite excellent candidates holding a PhD in Bioinformatics...including CV, brief statement of research interests and relevant data analysis experience, names and email addresses of at least 2 referees before November 11th, 2011 …

ASSET ASSET

updated 14.2 years ago • Mark Robinson

__The error info is just like__ :Error in checkProjectInput(project) :   Please set a valid project argument from the column id above. Project TARGET-AML was not found

software error tcgabiolinks

updated 8.1 years ago • sechenmo

Hello! I work with a nonmodel organism that does have a valid KEGG species code listed here: https://www.genome.jp/kegg/pathway.html This is the command I tried using: ```r test <- pathview...Hello! I work with a nonmodel organism that does have a valid KEGG species code listed here: https://www.genome.jp/kegg/pathway.html This is the command I tried using: ```r test &a…

KEGGREST KEGG gage pathview

updated 3.3 years ago • nute11a

a message : <pre> Error in .testForValidKeys(x, keys, keytype) : None of the keys entered are valid keys for 'PROBEID'. Please use the keys method to see a listing of valid arguments.</pre> May i know what is going wrong here

r codelink annotation annotationdbi

updated 10.6 years ago • Agaz Hussain Wani

microarray analysis using Limma and bioconductor. >I was searching the mailing list, and saw your name as one who >assist many people with their analysis. >I have a simple factorial design which I build the design and &gt...grateful is you could give me your opinion. > >I have two factors, one is strain with three levels (C,D,S), and a >treatment fact…

Microarray GO limma Microarray GO limma

updated 14.8 years ago • Naomi Altman

that DESeq2 seems to handle contrasts of count data oddly if all individuals belonging to the factor levels being contrasted have 0 counts. Below is some dummy code, with values taken from my data. There are two genes, eight individuals

deseq2 rnaseq r

updated 10.8 years ago • tw372

chromosome\_name", "start\_position", "end\_position", "external\_gene\_name", "go\_id", "name\_1006"), silence=TRUE)_ __Error: There is no feature column in annotatedPeak or               annotatedPeak

software error annotation

updated 9.0 years ago • jmKeith

storageMode: lockedEnvironment) >> assayData: 500 features, 154 samples >> element names: exprs >> protocolData: none >> phenoData >> sampleNames: GSM101849 GSM101851 ... GSM327326 (154 total) >> varLabels...object)' >> Annotation: hgu133plus2 >> Warning messages: >> 1: In…

Microarray GO Cancer Colon affy limma Microarray GO Cancer Colon affy limma

updated 14.4 years ago • James W. MacDonald

from it... readPlateList <- function(filename, path=dirname(filename), name, importFun, verbose=interactive()) { file <- basename(filename) dfiles <- dir(path) if(!(is.character(path)&&length(path...1)) stop("'path' must be character of…

GO Cancer cellHTS cellHTS2 GO Cancer cellHTS cellHTS2

updated 17.1 years ago • Florian Hahne

Hi, I am trying to import RSEM output (either gene or transcript level output) using txtimport. However, while running RSEM I used the option of append names which concatenates gene names

RSEM txtimport

updated 7.5 years ago • gat2010

snippet of code to run and identify more precisely where the problem comes from). > What is the name short name for R. Izarry et al. method ? I don't like avgdiff too much so I would like to use this one or LiWong's. Unlike for 'normalize...via Cel.container) are not completely merged (yet) for expression value computation from the probe level data. Slight difference remain between them.…

probe affy probe affy

updated 23.6 years ago • Laurent Gautier

Hello, I have a complex time-series RNA-seq expression dataset which I'm currently trying to analyse using DESeq2. I have two plant species, grown under two nitrate levels along six days of a heat wave experiment (a day before the heat exposure, three days of heat exposure, and two days of recovery). I also have the data from the last day, of plants (both species, with either nutrient …

deseq2

updated 9.2 years ago • giltu1

dataset = dataset, mart = mart) : #The given dataset: rnorvegicus_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. listDatasets(ensemblmart113) #no rnorvegicus_gene_ensembl

Rattus_norvegicus biomaRt

updated 13 months ago • Benjamin

Warning messages: 1: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 2: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 3: In curl::curl_fetch_disk...url, x$path, handle = handle) : progress callback must return boolean 4: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress …

annotationhub dependencies

updated 10.0 years ago • dalloliogm

library(limma) conditions <- data.trusted.eset$condition condition <- factor(conditions, levels(condition)[c(2,1)]) pairs <- factor(rep(1:13, each = 2)) design <- model.matrix(~condition+pairs) fit <- lmFit(data.trusted.eset...2)) design <- model.matrix(~0 +f +pairs) fit <- lmFit(data.trusted.eset, design) head(names$coefficients) contra…

limma microarray multiple factor design paired

updated 10.8 years ago • svlachavas

Thanks you very much for your attention.   ___cont.matrix<- makeContrasts (TGFbeta-Control, levels=design)___ _or_ ___cont.matrix<- makeContrasts (SSc – Control, levels=design)___ _instead_ ___cont.matrix<- makeContrasts...c('TGFbeta-Control', 'SSc - Control'), levels=design)___

microarray R

updated 7.3 years ago • morteza.hadizade

<div class="preformatted">Hello Limma developers and users, (sorry for the long posting) Today I encountered a similar problem as the one that was reported by Jason Skelton. I'm using Limma version 1.5.7 and R 1.8.1 on Windows XP platform. I have 16 slides divided into four comparisons (four in each). Each array contains 30 000 elements, representing 15 000 probes printed in duplicate (…

limma limma

updated 21.7 years ago • Valtteri Wirta

GDCquery(paste0("TCGA-", tumor), data.category = "Simple Nucleotide Variation", ': Please set a valid workflow.type argument from the list below: => Aliquot Ensemble Somatic Variant Merging and Masking ________________________________________________

maf R

updated 3.7 years ago • misslubblys

Hello, I then run into trouble when I attempt to create the summary object. This is the command I used: fast5files\_Summary <- readFast5Summary(fast5files) And I get the following error: <pre> Checking file validity</pre> <pre> Reading Channel Data</pre> <pre> Reading Raw Data</pre> <pre> Reading Template Data</pre> <pre> Re…

R sequencing preprocessing bioconductor

updated 10.0 years ago • mariandhore

ExpressionSet (storageMode: lockedEnvironment) assayData: 18952 features, 35 samples element names: exprs phenoData rowNames: E1E1_DrosophilaGenome2.0.CEL, E1E2_DrosophilaGenome2.0.CEL, .., R2W5_DrosophilaGenome2.0.CEL...I see that POP: arbitrary numbering ET: arbitrary numbering - Does it mean that factors' levels (such as POP: E1_2, M1_2, R1_2 and ET: E, W) are incorrectly as…

Survival cdf multtest affy factDesign biomaRt Survival cdf multtest affy factDesign

updated 17.5 years ago • Glazko, Galina

gtf", annotationFile = "genes.gtf", : Your organism has no mapping defined to perform the validity check for the UCSC compliance of the chromosome name. Defined organism's mapping can be listed using the 'knownOrganisms...function. To benefit from the validity check, you can provide a 'chr.map' to your 'easyRNASeq' function call. As you did not do so, 'validity.check' is turned off

Annotation Organism easyRNASeq Annotation Organism easyRNASeq

updated 12.8 years ago • Bayles, Darrell

Dear Maintainers As announced earlier this year, Bioconductor is moving version control systems from SVN to Git. ## The plan --- * Software, experiment data, and workflow packages will be maintained as git repositories created to capture the full commit history of each package. (the commit history of the 'data\_store' portion of data experiment packages will unfortunately not carry forward …

git svn infrastructure bioconductor News

updated 8.4 years ago • nitesh.turaga

**Data Scientist / Bioinformatician / Statistician** ---------------------------------------------------- **Location**: UCSF Mission Bay (Joan and Sanford I. Weill Neurosciences Building) **Department**: Psychiatry and Behavioral Sciences **Hours**: Monday - Friday, 9:00 am - 5:00 pm. Hybrid option available. ****JOB OVERVIEW:**** The laboratory of Matt State at the Universit…

programming datascientist psychiatry bioinformatics JobPosting

updated 2.1 years ago • Belinda