Bioconductor Forum

Hi all, I have a problem in figuring out how to include the batch effects in the design formula of DESeq. In particular I have to test the effect of one condition (Low protein diet vs Control diet) on gene expression over 48 mouse liver samples (24 for each condition). The problem is that I sequenced the samples in two separate batches (always keeping Treated vs Control in each batch) and d…

DESeq2 BatchEffect RNASeq

updated 3.1 years ago • Flavio

Error in combine_vars(data, params$plot_env, cols, drop = params$drop) : At least one layer must contain all variables used for facetting In addition: Warning messages: 1: In .Seqinfo.mergexy(x, y) : The 2 combined objects...have no sequence levels in common. (Use suppressWarnings() to suppress this warning.) 2: In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence...…

fourcseq

updated 8.4 years ago • rustavo

nor can I find a tool that can take an accession number and translate it into its organism's name. I am using R. Thank you for any help, J. Denton edit for clarification: for the accession number translation, an example would

AccNo OrgDb convert Organismname RStudio

updated 2.1 years ago • j_denton

It seems as though it is necessary for a column name (e.g., a channel) to match exactly the desc keyword in order for the function to work.  I think a workaround would be to...It seems as though it is necessary for a column name (e.g., a channel) to match exactly the desc keyword in order for the function to work.  I think a workaround would be to change the "desc" keyword in $P…

flowFit parentFitting(x channel flowcore flowCore

updated 11.2 years ago • erickttr

<div class="preformatted">Hello, I'd like to make clear how the 'Heat Map for Genes in Dataset' which is one of plots in the '(project name).global.plots.pdf' and is generated by the Gene Set Enrichment Analysis R code (GSEA.1.0.R)? The code is available as R-GSEA...d like to make clear how the 'Heat Map for Genes in Dataset' which is one of plots in the '(project name).global.plots.pdf' a…

Genetics Clustering DECIPHER Genetics Clustering DECIPHER

updated 15.7 years ago • Radek Blatny

Checking samples table... Populating samples table... Error: Column name mismatch. In addition: There were 50 or more warnings (use warnings() to see the first 50) Session info: sessionInfo() R version

cummeRbund

updated 8.2 years ago • sdhutchins

in listFilters(mart, what = "type") : The function argument 'what' contains an invalid value: type Valid are: name, description, options, fullDescription, filters5, filters6 I checked with listFilters(ensembl) and ?getBM, and

SNP GO hgu133a SNP GO hgu133a

updated 16.0 years ago • Tim Smith

nbsp;“getUniverseHelper(probes, datPkg, entrezIds) :   After filtering, there are no valid IDs that can be used as the Gene universe.   Check input values to confirm they are the same type as the central ID used...unique(goFrameData$frame.gene_id) >genes=c(1:5) >params <- GSEAGOHyperGParams(name="My Custom GSEA based annot Params", gene…

GOstats

updated 10.8 years ago • doodlehzq

answered my question, so much so considering that one of my factors (i.e. time) presents multiple levels, and not just two. Is there any way to get the triple interaction out of this? IF so, should I always go through the makeContrast

RNASeq limma voom anova

updated 8.4 years ago • David Rengel

gt; summarizeToGene (tximeta)`. In the code, the nf-core team defines the pattern for file names based on the quantification type and imports the transcript-level quantifications using `tximport`. They also create...a `SummarizedExperiment` object and process gene-level data using `summarizeToGene` if a mapping (`tx2gene`) is available. The nf-core team uses `gene_counts_length_scaled.tsv

tximportData summarizeToGene tximport DESeq2 salmon

updated 13 months ago • LuciaNhu

GO: ``` library(GEOquery) e = getGEO("GSE34313")[[1]] e$condition = e$characteristics_ch1.2 levels(e$condition) = c("dex24","dex4","control") table(e$condition) names(fData(e)) fData(e)$GO_ID[1:4] lvls = c("control", "dex4") es = e[,e$condition...in% lvls] es$condition = factor(es$condition, levels=lvls) library(limma) library(qvalue) design = model.matrix(~ es$condition) **fit = lmFit(es, desig…

roast-function

updated 3.9 years ago • leonardorosas2001

I am unsure how to interpret, i.e. should I be worried by it? The VCF written to disk appears to be valid. Many thanks for your help. ## Code > library(VariantAnnotation) > vcf <- readVcf(file = 'UnifiedGenotyper.autosomal.snps.indels.vcf.gz...GT PL rownames(292155): chr1:3003110 chr1:3012398 ... chr19:61340696 chr19:61340708 rowData values names(1): paramRangeID colnames…

VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation

updated 13.1 years ago • Peter Hickey

get the amino acid change by inputting the gff3 file to make a TxDB object and get variants on gene level. But I cant get this to work when genes consist of multiple exons or spliced genes. In some gff3 files I see the exon, mRNA

VariantAnnotation

updated 4.4 years ago • Kasper_holm2

ExpressionSet (storageMode: lockedEnvironment) assayData: 12135 features, 200 samples element names: exprs protocolData: none phenoData sampleNames: 21001 21004 ... 22078 (200 total) varLabels: ID idx ... U_MoBT (53 total) varMetadata...the regulon objects... Error in tapply(1:nrow(tmp), tmp$tf, function(pos, tmp) { : arguments must have same length ##Looking at source co…

viper

updated 6.3 years ago • maya.kappil

Production Bioinformatics _Reports To_: NGS platform manager _Salary:_ Commensurate with level of experience _Hours:_ 37.5 Hours per Week _Status:_ Full-Time The Atlantic Cancer Research Institute (ACRI...Bachelor’s or master’s degree in related discipline, with demonstrated experience in the skill set; * Must have advanced skills in Unix shell programming enviro…

cancer bioinformatics bioinformatician job sequencing Job

updated 7.3 years ago • gabriel.wajnberg

from tx2gene: 36704 summarizing abundance summarizing counts summarizing length Error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE In addition: Warning messages: 1: In rowsum.default(abundanceMatTx...3: In rowsum.default(abundanceMatTx * lengthMatTx, geneId) : missing values for 'group' 4: In names(aveLengthSampGene) == rownames(lengthMat) : longer object length …

tximport salmon R bioconductor

updated 8.4 years ago • macmanes

I've got a dataframe of the file paths of the data and the names. This is fine ```r k = tximeta(coldata = data.frame(files = m, names = names(m)), type = 'oarfish') y <- scaleInfReps(k) # scales counts y <- labelKeep...condition") # simplest Swish case ``` The errors start appearing here: ``` # run on the transcript-level dataset iso <- isoformProportions(y) Error in isofo…

fishpond tximport tximeta

updated 10 months ago • brown.annaleigh

45101,adjust.method="BH",sort.by="B" ) names(comp1) names(comp1)[1]="Probe" probeids=comp1$Probe aaf.handler() anncols<-aaf.handler()[c(1:5,11:12)] anncols comp1table&lt...comp2<-topTable(fit,coef=2,number=45101,adjust.method="BH",sort.by="B" ) names(comp2) names(comp2)[1]="Probe" probeids=comp2$Probe aaf.handler() anncols<-aaf.handler()[c(1:5,11:12)] anncols comp2t…

GO Cancer mouse4302 limma GO Cancer mouse4302 limma

updated 12.7 years ago • Richard Friedman

and 7 value columns across 1 space space ranges | type source phase strand ID Name score <factor> <iranges> | <factor> <factor> <factor> <factor> <character> <character> <numeric> 1 2L [7529, 9484] | gene FlyBase 0 NA FBgn0031208...textConnection(gff.str),asRangedData=FALSE) Error in s…

updated 13.6 years ago • Malcolm Cook

cover "automatically" the cases where the covariate is a factor, a continuous one or also where the levels are more than two. Quick check I am doing it right, according to the documentation:  factor -> contrast = the 3-element...vector  numeric -> name = the character name of the numeric  more than 2 levels -> rerun DESeq wit…

deseq2

updated 9.1 years ago • Federico Marini

filtered the low count <5 before running the analysis. ### result for Sex (F as reference level) res_Sex <-results(dds_full, name="Sex_M_vs_F") summary(res_Sex) out of 15895 with nonzero total read count adjusted p

deseq2

updated 6.8 years ago • sharmila.ahmad

opt)) { if (is.na(files) || is.null(files)) { stop("Error: the file name is NA or NULL.") } else { stop(paste0("Error: the file name must be a character vector. The current input is ", class(files))) } } else { if (is.na...contains the internal splitor of featureCounts (\\…

Rsubread featurecounts coercion

updated 4.5 years ago • Konstantinos Yeles

Hello, I am running DESeq2 with this metadata table - | Condition | Time | Batch | |-----------|------|-------| | Control | 0h | 1 | | Control | 12h | 1 | | Control | 24h | 1 | | Control | 0h | 2 | | Control | 12h | 2 | | Control | 24h | 2 | | Control | 0h | 3 | | Control | 12h | 3 | | Control | 24h | 3 | | Control | 0h | 4 …

DESeq2

updated 12 months ago • bhandary.8590

cell lines not responders to the treatment (responders vs not resonders). Here the sampleTable: Name Cell_line condition cell_line1_rep1 Cell_line_1 RESPONDERS cell_line2_rep1 Cell_line_2 NOT_responders cell_line3_rep1...or interaction terms in the design formula are linear combinations of the others and must be removed. Please read the vi…

DESeq2

updated 4.6 years ago • dequattro.concetta

in the bhc package. Anyone know what I'm doing?  In this case, candidates is a list of gene names that I am extracting from a larger frame of all genes.  Plotting the dendrogram works fine.  `` rawCounts = read.table...0, numThreads=10, verbose=TRUE) ``   `` heatmap(hc2) `` Error in heatmap(hc2) : 'x' must be a numeric matrix   Cheers …

bhc

updated 10.6 years ago • b.curran

phenoData = phenoData ) In R 2.9.2 we are getting the following error message: error in sample names<= tmp value = c (sample 1 sample 2 sample 3) value length (8) must equal sample number in assay data (0). I have a question for lumi

lumi lumi

updated 16.2 years ago • Michal Blazejczyk

<div class="preformatted">Yeah, I have the same problem. There are lots of ready-made search solutions out there, and I hope the list admins eventually adopt one of them. In the meantime, I do my searches "off-line". I downloaded all the archives to my computer and then installed WinGrep (http://www.wingrep.com/). As the name suggests, it allows you to use regular expressions. Furthermore, …

updated 21.9 years ago • Alex F. Bokov

query with getBM(), it tells me my mart doesn’t exist. ```r Error in martCheck(mart) : You must provide a valid Mart object. To create a Mart object use the function: useMart. Check ?useMart for more information. ``` I have

biomaRt

updated 3.2 years ago • Laurel

<div class="preformatted">Hello all, Is there anyway to retrieve the gene symbols, full names (discription), or other gene information, given a list of Entrez Gene IDs (or the LocusLink) in Bioconductor. Obviously, one...div class="preformatted">Hello all, Is there anyway to retrieve the gene symbols, full names (discription), or other gene information, given a list of Entrez Gene IDs (o…

Annotation Annotation

updated 19.4 years ago • Luo Weijun

field ]] } else { obj[[ field ]] } } Then, call .get.column(obj,'name') wherever I used to simply use obj[['name']] before introducing GenomicRanges? Tim On 27/08/2010 15:02, "Martin Morgan" <mtmorgan...gt; >>>> # Extract the name field from each of these objects using [[ >>>> >>&am…

IRanges IRanges

updated 15.3 years ago • Tim Yates

error peaks1 = RangedData(IRanges(start = c(1, 100, 200), end = c(2, 101, 201), names = c("Site1", "Site2", "Site3")), space = c("1", "1", "1"), strand=as.integer(1),feature=c("a","b","f")) peaks2 = RangedData(IRanges(start = c(1, 100, 200), end = c(2, 101...201), names = c("Site1", "Site2", "Site3")), space = c("2", "2", "2"),…

GO BSgenome BSgenome ChIPpeakAnno GO BSgenome BSgenome ChIPpeakAnno

updated 12.5 years ago • Vince Schulz

probabilistically across large biomedical datasets. Although traditional linkage variables such as names or zip codes will be available in some datasets, the software must also handle data that contain only genomic sequences...grants). Thus, there will be synergies between the two projects. __Requirements__: Candidates must have a PhD or other advanced degree in computer science, biomedical inf…

Probabilistic Algorithms Big Data Job

updated 10.6 years ago • Doe, Aimee

lt;- DESeqDataSetFromTximport(txi, sampleTable, ~tissue)<br/> Error in checkSlotAssignment(object, name, value) : <br/>   assignment of an object of class "NULL" is not valid for slot 'NAMES' in an object of class "DESeqDataSet

deseq2 tximport

updated 8.6 years ago • JWCarlson

LFCs in my model but I keep generating an error. <pre> resLFCint <- lfcShrink(dds, res = res, name="Cov1.Conditioncase", type="apeglm")) using 'apeglm' for LFC shrinkage Error: !missing(coef) is not TRUE design ~ Age + Gender + Cov3...Condition + Cov1:Condition </pre> where Cov1, Cov2 and Cov3 are all continuous variables and levels of Condition are treated and untreat…

deseq2 interaction term

updated 7.2 years ago • Cece

<div class="preformatted">Hello list, I am trying to use topGO for GO enrichment analysis. I have data from an array which is still not supported by BioC (maize array). I have a mapping of genes to GO terms named go_list: $TM00000001 [1] "GO:0009058" "GO:0016757" $TM00000002 [1] "GO:0003700" "GO:0007275" "GO:0005634" "GO:0009414" "GO:0016563" [6] "GO:0009737...an array which is still …

Annotation GO topGO Annotation GO topGO

updated 17.2 years ago • Heike Pospisil

training on 100s of MRI scans with paired pathology and genomics data • Apply these methods to validation cohorts in the diagnostic pathway to test the impact of AI approaches on diagnostic accuracy • Explore the added...apply:__ Applications, including a CV and a Reasons for Applying statement (2,500 character limit), must be made via the University of Cambridge Graduate Admissions websit…

PhD cancer deep learning computational biology Job

updated 7.0 years ago • Shamith.Samarajiwa

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...datasetconfigversion="0.6" requestid="biomaRt" uniquerows="1" virtualschemaname="default"> <dataset name="hsapiens_gene_ensemb…

biomaRt biomaRt

updated 13.6 years ago • Lisa Hopcroft

annotation annotations <- prepareAnnotations("./refgenome/tn2.gtf") #output : transcript names are not unique, only one transcript per ID will be kept Error in .local(x, ..., value = value) : 1587 rows in value to replace 1574rows...Model Prediction Score) A high NDR threshold is being recommended by Bambu indicating high levels of novel transcripts, limiting the pe…

txdb bambu

updated 2.5 years ago • camilia.savitri

lt;- readMappings (file = "my\_M1.SINV.gene\_GO",sep = "\\t", IDsep = ",") geneUniverse <- names(geneID2GO) genesOfInterest <- read.table("interestinggenes.txt",header=FALSE) genesOfInterest <- as.character...genesOfInterest$V1) geneList <- factor(as.integer(geneUniverse %in% genesOfInterest),levels =c(0,1)) names(geneList) <- geneUniverse plot(geneLis…

topgo

updated 9.4 years ago • pninasmail

Hi! So I'm basically asking the same question as [this post][1], but have a slightly more complex design and want to make sure I'm setting up the proper contrasts. I have samples from two different genotypes (B6 & TCR) reared in 3 stress conditions (no stress, NS; single hit, SH; double hit, DH). I am interested in the main effect of genotype, the main effect of stress, and the interact…

DESeq2 contrasts

updated 3.8 years ago • Mir

1L, 1L, 1L, 1L, 2L, 2L), contrasts = structure(list( S = "contr.treatment", Batch = "contr.sum"), .Names = c("S", "Batch"))) There are 12 conditions, and the 12-condition experiment is replicated 3 times. One thing I'd like to do with this...dataset is to identify a set of "housekeeping" genes specific to this data, i.e. genes whose levels do not change very much across all the samples. Is …

ASSIGN ASSIGN

updated 12.8 years ago • Ryan C. Thompson

in combine_CompressedList_objects(class(x), objects, use.names = FALSE, : the objects to combine must be CompressedList objects (or NULLs)</pre> Any help about how to solve this / what I am doing wrong is much appreciated :) Thanks...txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene ## needs to have 2 meta columns: score, name exo <- exonicParts(txdb, linked.to.single.gene.o…

genomicranges genomicfeatures

updated 8.0 years ago • Fabian Grammes

results table contrasting conditions A and B in the next chunk. We can do this by using either the `name` or the `contrast` argument. Later on we would be interested in the other contrasts with condition C as well, but for purposes...of illustration I leave that out in this example. ``` dds <- DESeq(dds) # call results() w/ name and contrast arguments res.cont <- results(dds,…

deseq2

updated 6.4 years ago • Vincent de Bakker

transcript (gene) version\]". I keep getting an error message that says the probe ids are not valid for that database. Are these numbers not actually probe ids? How do I know how to associate them to the mgi\_symbol?&nbsp...Error in .testForValidKeys(x, keys, keytype, fks) :    None of the keys entered are valid keys for 'PROBEID'. Please use the keys method to see a list…

annotation affymetrix

updated 7.7 years ago • trhood

Hello, I have a small dataset with 3 replicates per condition. One condition is a gene over-expression, the other is a control. I'm used to run DESeq2 with betaPrior = True to have a comparability with the 'old' DESeq2 behavior. I can't apply this old workflow because the expression differences between my conditions it quite small and one gene, namely the over-expressed ![](https://ibb.…

deseq2 lfcshrink betaprior

updated 7.4 years ago • mat.lesche

Hi everyone, We apologize for the recent spam attack. There were hundreds of posts within a very short time, making the site unusable. It was especially painful for those users who received every post via email.  The site was also shut down for several hours as a preventative measure, until we were able to deal with the problem.  We are committed to fighting spam and keeping t…

security spam News

updated 9.6 years ago • Dan Tenenbaum

in listFilters(mart, what = "type") : The function argument 'what' contains an invalid value: type Valid are: name, description, options, fullDescription, filters5, filters6 How should I modify the query? If I use the query with

GO hgu133a GO hgu133a

updated 16.1 years ago • Tim Smith

Dear all, I used Deseq2 to analyse differential gene expression: I have 2 factors: - phenotype (2 levels: slow and fast) - timepoint (3 levels: RT, 15, 90) Overall, I want to know which genes are differentially expressed between the...timepoint + phenotype:timepoint)  colData(dds)$timepoint <-factor(colData(dds)$timepoint, levels=c("RT", "15", "90")) colData(dds)$phenotype …

deseq2 multiple factor design results

updated 9.5 years ago • koeniger

cpm(dge, log=TRUE) par(mfrow=c(1,2)) col.group <- group col.group <- as.factor(col.group) levels(col.group) <- wes_palette(nlevels(col.group), name="Darjeeling1") col.group <- as.character(col.group) plotMDS(lcpm...gt; par(mfrow=c(1,2)) > col.group <- group > col.group <- as.factor(col.group) > levels(col.group) <- wes…

limma MultidimensionalScaling

updated 3.0 years ago • Katharina

will automatically extract results for the last variable in the design formula, and for the last level of this variable over the first level if this variable is a factor.â But otherwise, no it doesn't make a difference if you...terms in the design formula. If you are using DESeq2 v1.2 you can pull out the effects by 'name' argument to results(), using a name in resultsNames(dds). In DESeq2 &…

DESeq2 DESeq2

updated 11.7 years ago • Michael Love

data and I thought it should be possible to hand "geneIds" and universeGeneIds in the form of probe names (here IPI IDs) to the hyperGTest function. If I do so I always get the error: # Error in getUniverseHelper(probes, datPkg, entrezIds

Annotation probe Annotation probe

updated 17.5 years ago • Johannes Graumann

arrays may be fine when there are many random proteins to bring between array intensities to similar levels. However it seems to me (I am relatively new to array analysis so I may be wrong) that if we have specifically chosen proteins...expression in some samples and high expression in other samples that this normalisation would not be valid ,as the assumption for this normalisation is that ge…

limma microarray r

updated 6.9 years ago • reubenmcgregor88

model with 3 factors: patient(patients A to I, to account for biological differences), condition(levels "Other_CD4", "VbOther" and "Clone", in that order) and timepoint (T1 and T2). The comparisons I am interested in are really "Other...H:/R/htseq_counts_experiment_5/metadata_5.csv") metadata_5 <-as.data.frame(metadata_5) #column1 name comes out bit weird- this changes the name names(met…

DESeq2

updated 4.2 years ago • Sonia

it: ``` Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'TXNAME'. Please use the keys method to see a listing of valid arguments. ``` The function: ```r transcriptToSymbolAndDescription

RNASeq

updated 3.5 years ago • becker.jemima

I am filtering based on variance how much filtering I can do and still call my DE results with limma 'valid'. For instance, if I select the top 10% or 5% of the most variable genes by the co efficient of variation can I still do differential...expression on different subgroups of the data set and call my conclusions valid? I think the answer to this is yes, because I am not specifically selecting…

limma microarray normalization

updated 10.4 years ago • chris86

Error Message #Error in .testForValidKeys(x, keys, keytype, fks) : # None of the keys entered are valid keys for 'SYMBOL'. Please use the keys method to see a listing of valid arguments. ``` Given that I am working in Human the org.Hs.eg.db

clusterProfiler

updated 4.9 years ago • Andrea

process of base calling is the sequencing itself which tells us the intensity of the noticed base is valid enough to be added to our sequence or not) also determines the process of sequencing so there should not be any differences...between it and the chastity filtering which also determines the validity of sequencing. Am I right? Thanks a lot in advance Narges</div

Sequencing PROcess Sequencing PROcess

updated 13.4 years ago • Fatemehsadat Seyednasrollah

is: Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ALIAS'. Please use the keys method to see a listing of valid arguments. GG is supposed to contain GENE IDs for human

limma annotation Gene

updated 5.8 years ago • omarrafiqued

below is the correct approach for importing (and subsequently passing on to `DESeq2`) expression levels quantified using `Salmon` with the transcript-gene relationship given by a two column `data.frame` named `tx2gene`? **(1):** ``` txi

DESeq2 tximport salmon

updated 2.9 years ago • Dunois

contrast.matrix <- makeContrasts(4day,9day,14day,19day,14daf,19daf,4daf,9daf,control,4day -19day,levels=design) Error: syntax error What am I doing wrong? thanks Simon. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available

limma limma

updated 21.9 years ago • Simon Melov