Bioconductor Forum

According to the GenomicFeatures annotation and this [post][1] it was a conscious decision to not include gene_name in the TxDb objects from the GenomicFeatures package. Is the decision of not including gene names something that could be brought up again? I think we can all agree that in the end the majority of end users would like gene...in the TxDb objects from the GenomicFeatures packag…

Bioconductor GenomicFeatures TxDB

updated 5.1 years ago • k.vitting.seerup

<div class="preformatted"> Dear list, I am not sure the correct way to interpret the nbinomLRT results in multiple level factors condition. Here is a toy example. I would to find DE genes after controlling batch effect in the experiments, in...Dear list, I am not sure the correct way to interpret the nbinomLRT results in multiple level factors condition. Here is a toy example. I would to f…

updated 11.3 years ago • shao

div class="preformatted">Dear list, I'm looking for a way to get the names of all Gene Ontology terms for Biological Processes at level 5 as well as the genes (human gene symbols) annotated to each...of the level 5 GO terms. I have tried to query the DAVID knowledgebase, but the online tool doesn't seem to respond to any requests. Hence

GO GO

updated 12.5 years ago • Peter Davidsen

modal omic data (incl. DNA sequence, epigenome transcriptome, proteome) in drug target discovery and validation. The position is part of a cooperation with Cellzome, a company located on the campus of EMBL, and offers the opportunity...requires outstanding quantitative and analytical skills. We are looking for candidates with PhD-level education in mathematics, statistics, physics, computer sc…

job Job

updated 9.7 years ago • Wolfgang Huber

dev <- computeDeviations(object = rse, annotations = motif_mm) ``` ``` Error in names(res) <- nms : 'names' attribute [386] must be the same length as the vector [302] In addition: Warning message: stop worker failed...dim: 4446140 386 metadata(0): assays(1): motifMatches rownames: NULL rowData names(2): name bias colnames(386): MA0025.1_NFIL3 MA0030.1_FOXF2 ... MA090…

chromVAR computeDeviations

updated 5.4 years ago • mkarimzadeh

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updated 18.3 years ago • Li Xiao

from a DESeqDataSet on which I've called nbinomWaldTest specifying the factor (treatment) and levels of interest (a versus b). The host plant species contrast isn't as straightforward. I have at least two options. The simplest...being: <pre> results(dds.bacterial.taxa, name="species1")</pre> Species 1 is one of my host plant species and appears as an element of resultsNames(dds.bac…

deseq2 lfce contrast

updated 8.8 years ago • crfitzpat

already use edgeR and DESeq2 and would add limma soon. Now I wonder whether I can use these tools to validate the identified genes? Of course I need wet lab validation to some extent (qPCR for some interesting genes will be started

edger limma deseq2 rnaseq

updated 9.4 years ago • WouterDeCoster

computing iqlr centering* `Error in apply(reads.clr[these.rows, ], 2, function(x) { :` ` dim(X) must have a positive length` `Calls: aldex.clr ... aldex.clr.function -> aldex.set.mode -> iqlr.features -> apply` *Execution...r # "oral_table" is a data frame with samples in columns and genera in rows (with the genera names as row names) ALDEx2_object = aldex.clr(oral_tabl…

Metagenomics IQLR ALDEx2

updated 3.0 years ago • cwarden45

interest (there are 62 of them). What should I write to make such a table (where should I place the names of the genes)? My code at the moment: Code should be placed in three backticks as shown below ``` gset <- getGEO("GSE24742", GSEMatrix...TRUE, AnnotGPL=TRUE) if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1 gset <- gset[…

DifferentialExpression limma R TissueMicroarrayData

updated 2.9 years ago • Элина

Error in map_x_colnames_to_object_colnames(colnames(object)) : the DataFrame objects to rbind must have the same colnames ``` What other column names could be causing the error message? Perhaps the error message could be

VariantAnnotation VCF

updated 6.5 years ago • Dario Strbenac

em>I am trying to do a heatmap, but I can't see what I am doing wrong. I get the error message: `x' must be a numeric matrix.</em></pre> library(limma) library(Biobase) setwd("/export/work/geneSTdataset") expr.rma <- read.table("tmp...44797,1:6\] exprs(vv) heatmap(exprs(vv)) Error:  <pre> Error in heatmap(exprs(vv)) : 'x' must be a numeric matrix&…

r heatmap numericmatrix

updated 9.7 years ago • Biologist

Hi all, I have a multi-level design for an [RRBS](https://en.wikipedia.org/wiki/Reduced_representation_bisulfite_sequencing) experiment, which...is identical to the multi-level design mentioned in Section 9.7 of [`limma`'s User Guide](https://www.bioconductor.org/packages/devel/bioc/vignettes...to make comparisons across `tissue`s and `disease` groups while blocking for `patient` IDs. (I …

edgeR voomLmFit limma duplicateCorrelation voom

updated 4.0 years ago • altintas.ali

reproduce the error <https://gist.github.com/pauca/f3b843d1939461b8ea2b83ec4b332b04> The Fastq is valid according to fqtools fqtools validate corrupted.fastq OK Thanks for any advice &nbsp

Rqc

updated 8.9 years ago • paucarrio

<div class="preformatted">Hi I am still new to EdgeR and am using it to do pairwise comparisons of RNA seq data. I just realized that the sign of the fold change will be determined by how you label the samples in groups. So if I have T1 and T2 as my two groups, it is labeled in that order in d$samples, and in the levels reported in d$samples$group. If I use as names T80 and T60 d$sample…

edgeR edgeR

updated 13.6 years ago • Spollen, William G.

I try and use the importMAGEML() function, I get this error: Error in checkSlotAssignment(object, name, value) : Assignment of an object of class "list" is not valid for slot "maLabels" in an object of class "marrayInfo"; is(value, "character...package: SJava Warning message: The Java machine is no longer initialized automatically. You must explicitly load it in: f(libname, pkgname) This email …

RMAGEML RMAGEML

updated 20.8 years ago • Dykema, Karl

aln) hits <- countOverlaps(aln,gnModel) counts <- countOverlaps(gnModel,aln[hits==5]) names(counts) <- names(gnModel) counts } counts <- sapply(bamFiles,counter,gnModel) Note: method with signature Vector#GRangesList...target signature GappedAlignments#GRangesList. "GappedAlignments#Vector" would also be valid Note: method with signature GRangesList#Vector chos…

RNASeq RNASeq

updated 12.3 years ago • Reema Singh

character.only=TRUE)}) Error in library(pkg, character.only = TRUE) : 'GolubRR' is not a valid package -- installed < 2.0.0? I am running R from the following: R v.2.0.0 Windows XP Dell Pent IV Would you happen to know

updated 21.0 years ago • Samantha Ying

avgTxLength ... H cooks rownames(11060): FBgn0000003 FBgn0000008 ... FBgn0288846 FBgn0288856 rowData names(66): baseMean baseVar ... deviance maxCooks colnames(198): 1 2 ... 1291 1425 colData names(10): library sample ... condition ``` the 'rownames...an extra column in res_log2FC which consists in a concatenation of the accession number and gene name : genes <- res_log2FC$row gene_name…

DESeq2 ComplexHeatmap

updated 6 months ago • caroline.zanchi

0.995723495236492 NA And for these ensembl IDs I have got the gene name via a `biomaRt` query: > head(G_list) ensembl_gene_id hgnc_symbol ensembl_gene_id_version 1 ENSG00000007923 DNAJC11...How do I now alter `res` so that the results of my DE analysis display the gene name (as given in `G_list`) rather than the ensembl ID? I have tried to use `mer…

DESeq2

updated 5.0 years ago • Linda

test.bw") > import.bw(test_bw) Error in stop_if_wrong_length(what, ans_len) : 'ranges' must have the length of the object to construct (9) or length 1 > > traceback() 11: stop(wmsg(what, " must have the length of the object...test_bw, which = mini, as = "RleList") Error in stop_if_wrong_length(what, ans_len) : 'ranges' must have the length of the object to construct (83…

rtracklayer

updated 3.4 years ago • bonob

this, but this is dependent on me being able to map the results from vsn. I am working on the probe level, so in other cases, where the results have been an affybatc, my solution to accessing the data has been to use the command...find any such information associated with these objects. I am able to utilise not only the probe name, but also the x and y positions on the chips too, but I cannot fin…

probe vsn probe vsn

updated 18.8 years ago • Karin Lagesen

I'm working with a non-model species so having genes' name is luxury I can't afford. I have my design matrix and choose one combination I'm interested: cont.matrix1 <- makeContrasts...GlandvsRoot=Leaf - Gland,levels=design) fit.cont <- contrasts.fit(fit, cont.matrix1) fit.cont <- eBayes(fit.cont) fit.cont <- eBayes(fit.cont) summa.fit...summa.fit) and when I w…

limma DEGreport Volcanoplot

updated 2.9 years ago • Mohammad

<div class="preformatted">Hello All, I wrote a script to analyse affymetrix data but its giving an error while using the topTable from limma: Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type I checked all the steps that might be causing the error but couldn't find out. So, I trimmed my script to minimal basic and it still giv…

updated 12.7 years ago • Atul Kakrana

object itself fails: > Data <- ReadAffy() > Data[1,] Error in checkSlotAssignment(object, name, value) : Value supplied is not valid for slot "pData", is(value, "data.frame") is not TRUE > Data[,1] Error in checkSlotAssignment...object, name, value) : Value supplied is not valid for slot "pData", is(value, "data.frame") is not TRUE Any pointers on wha…

cdf probe affy cdf probe affy

updated 23.6 years ago • Deepayan Sarkar

me, I have encounterd with one question about tximport. I have used tximport to import trancript-level abundance from Salmon to gene-level. now I want to choose some of significant genes for confirmation by RT-PCR. but I am...each gene has number of transcript. whether tximport summerize all trasncript of one gene to gene-level or even one of its transcript

tximport

updated 7.1 years ago • lkianmehr

But: t2 <- RangedData(IRanges(start=c(7828367, 7828552,4121953), end=c(7828402, 7828587, 4121988), names=c("a", "b", "c")), space=c("Chr1", "Chr1", "Chr3"), mapq=c(1,2,1),flag=c(3,4,5)) (Here, I would like to keep the read names along with their positions in the...gt; rbind(t2,t2) Error in validObject(.Object) : invalid class "RangedData" object: the names of the ranges must equal the ro…

IRanges IRanges

updated 16.3 years ago • Ulrike Goebel

p> <pre> Error in data.frame(row.names = colnames(countdata), condition) :    row names supplied are of the wrong length</pre> <p>Then, I tried running it without condition, which works. However, when I try to run...code>Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData</code><…

deseq2 R genomics

updated 7.8 years ago • mokunf

not mention the use of Tximport or any other tools but the read counts are already collapsed to gene-level, resulting in a matrix with gene names in the first column (e.g. TP53, A2M), genome-coordination in the second column (e.g. "chr17_7661779_7687550_...is no need for any prior data transformation since the counts are already collapsed to the gene level. so simply using the following codes sho…

DESeq2 tximport Kallisto TMM edgeR

updated 4.1 years ago • BioNovice247

with literature observations, but my question is whether the approach I took can be considered valid? Thanks

RNASeq

updated 2.9 years ago • SciencyKr

m.4374.path2.0 1A_I11_NT_comp46081_c0_seq2|m.4378.path1.0 rowRanges metadata column names(0): colnames(16): A-P56-1 A-P56-3 ... B-P67-4 D-P56-4 colData names(2): TREAT LAT</pre> 3) when I try to run DEseq(dds) I got this error; <pre> estimating...estimates Error in model.matrix.formula(design(object), data = colData(object)) : data must be a data.frame</pre> 4) I chec…

deseq2

updated 5.3 years ago • mdelrgg

for more than 2 genotypes simultaneously against each other, why is it still important to set a base level? If I set a base level, all the comparisons will be made against the base level, not against each other. To illustrate, I am...interested in comparing genotypeA, genotypeB, and genotypeC. If I set genotypeA as my base level, I will be comparing genotypeB and genotypeC against genotypeA. I wo…

updated 11.9 years ago • Guest User

arrays (MoEx-1_0) using xmapcore and would like to use the splicing index function to compare the levels of splicing in two conditions. It's documented here: http://svitsrv25.epfl.ch/R-doc/library/exonmap/html/si.html Unfortunately...ENSMUSG00000000001", "ENSMUSG00000000003"), gps=gps) and the error: Error in fix.by(by.y, y) : 'by' must specify valid column(s) In addition: Warning message: In…

exonmap xmapcore exonmap xmapcore

updated 15.2 years ago • Peter Saffrey

<div class="preformatted">Dear all, Currently£¬we are working with Affymetrix u133plus2 array and interested in classification disease/control using microarray data. We have identified a molecular signature and trained a svm-based classification model based on 200 samples (100 disease +100 control). We are satisfied with the model performance (sensibility/specificity) evaluated with cross…

Microarray Classification PROcess Microarray Classification PROcess

updated 16.0 years ago • qinghua.XU@as.biomerieux.com

package cannot properly handle condition (given by the 'sample\_1' and 'sample\_2' columns) names starting with numerics. Some methods handles it standard R style by adding an 'X' before the condition/sample name. Examples...cuffDB))   Other methods fails and end up with NA's ('<NA>' to be precise, the factor levels of these are however correct). I found this for methods…

cummerbund

updated 9.7 years ago • kristoffer.vittingseerup

matrix by putting the mutations in a factor variable along with the control. Now the variable has 4 levels (mutA, mutB, mutC, control) and I have set the "control" level as the first level. How do I make a contrast that detects DE elements...__ but "control" doesn't appear as a coefficient in the design matrix since it is the reference level. Is this: design <- model.matrix( ~ factor w…

diffrential expression limma makeContrasts

updated 7.4 years ago • S.Bamopoulos

div class="preformatted">Hello, I've done some analysis on a factorial design based on the probe level (affymetrix). The data was background corrected with RMA and normalized via quantiles, but no summarization of the probes...uses the array as a random effect): Y = B+D+T+P + BP + BD + BT B = Batch or Laboratory effect (3 levels) D = Dose (5 levels) T = Time (2 levels) P = Probe (~16 levels…

probe limma DOSE probe limma DOSE

updated 21.6 years ago • Arne.Muller@aventis.com

has the same start and end coordinates, but the CHR column shows chromosomes 1 and 2. One of these must be incorrect. I noticed the chromosome name format changed from 'chrX' to just 'X', and I imagine that has something to do with...the reordering of factor levels. Am I doing something wrong, or is this a bug? Thanks again for your help! <img alt="" src="https://i.imgur.com/2lyIgiz.png" st…

DiffBind

updated 7.1 years ago • jingyaq

<div class="preformatted">Hello friends, i am working on some SMD two color data for Toxoplasma gondii , i have done differential expression analysis. Now i want to annotate these genes, now the problem is that how can i convert the probe ID's to Gene names using annotation package and with what database because there is no database in bioconductor related to t. gondii. if i have to pick…

Annotation GO probe annotate convert Annotation GO probe annotate convert

updated 14.9 years ago • Budhayash Gautam

gmail.com=""> writes: > I would like to know how to evaluate a character string as a variable name > in R. Specifically, I need to "compute" the variable name in the phenoData > slot of an ExpressionSet object. > >> varLabels...Male Male Female Female Female Male Male Female [21] Male Female Male Male Female Female Levels: Female Male e.g…

Cancer Cancer

updated 16.6 years ago • Martin Morgan

is a matrix of RMA normalised expression values from some 400 Exon arrays summarized at the probeset level. We are only interested in the gene level and wondered if there is any way to summarize to the gene level from this starting

normalization oligo limma

updated 10.4 years ago • i.sudbery

dge <- estimateDisp(dge, design) Error in .compressWeights(y, weights) : weights must be finite positive values</pre>   As you can se no weight is out the rang 0-1 or infinite. <pre> > sum(is.infinite(dge$weights

edger estimatedispersions

updated 7.4 years ago • nonCodingGene

Hello together, hello Michael, I have an understanding problem using results(dds, ...) I have RNAseq data and a grouping of two conditions with interaction of time with the defined reference levels, see code below. And run the code as below. ```r coldata$Cond <- factor(coldata$Cond, levels = c("A","B")) coldata$Time <- factor(coldata$Time, levels = c("2","5","7")) formula = ~ C…

DESeq2

updated 2.2 years ago • Rockbar

client", directory = "./Data"). , and I found the following error : “Error: Results must have the same dimensions” Please advice. Thank you

TCGAbiolinks GDC dataset

updated 6.0 years ago • ph.shimaasherif

I was given a table of salmon transcript level quantifications for 75 samples and I am hoping to generate gene level summaries. I can create the database that describes...ensembl annotations) but does tximport or another tool have the ability to do the tx to gene level count conversion from the table as opposed to the multiple files that salmon normally outputs? Thanks, -Lauren

tximport deseq2

updated 6.4 years ago • ljmills

which I think need clarifcation I used a fairly common experimental design with a factor that has 3 levels and DM is initial reference level. <pre> coldata$Cond <- factor(coldata$Cond, levels = c('DM', 'DP', 'Co')) ddsdm <- DESeqDataSetFromMatrix...should and report the wrong results. 2a) This will even more confusion when one has more than two levels in a factor. For exa…

deseq2 lfcshrink relevel

updated 8.1 years ago • mat.lesche

variable. I am interested in finding DEG genes between PD and CR/PR with PD as the reference level. My design is: design(dds)=~Response Normally, in order to get the DEG result, I would call results(dds,contrast=c("Response...PD")) to retrieve the result. However, I am wondering about the result from calling results(dds,name="ResponsePRCR") which is supposed to give us the individual effect and…

DESeq2

updated 8.2 years ago • fkuo

between IP samples. If I do want to incorporate input control into my differential binding, is it valid to include that data as another factor in the design matrix and perform a difference of difference? So for every library...I would have a "IP" factor with two levels (IP/Input) and also a "sample" factor with two levels for treatment and control.  I am not very well versed in R, wou…

chip-seq differential binding analysis

updated 9.3 years ago • damian.kao

dds_all_corrected <- DESeq(prev_dds) ``` if I code `colData(prev_dds)` I corroborate I have 8 levels ```r > colData(prev_dds) DataFrame with 307 rows and 3 columns GroupPregnancy sizeFactor replaceable <factor> <numeric...5 5 5 6 6 5 5 5 5 5 5 5 5 6 6 5 5 5 5 5 5 6 5 6 5 5 6 5 5 5 5 5 5 6 6 6 6 5 6 6 [301] 6 5 …

Contrast factors levels

updated 3.1 years ago • Edgar

must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 6: In result_fetch(res@ptr, n = n) : SQL statements...must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 7: In result_fetch(res@ptr, n = n) : Then...in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have…

makeOrgPackage

updated 4.8 years ago • Eduardo Andres-Leon

for mydata' has been created. Error in svgStyleAttributes(style) : All SVG style attribute values must have length 1</pre> and when running a second time <pre> Error in gridsvg(name = "arrayQualityMetrics report for mydata/pca.svg...is as follows: <pre> 7: stop("Only one 'gridsvg' device may be used at a time") 6: gridsvg(name = "arrayQualityMetrics report for mydata/pca.…

arrayqualitymetrics svg software error

updated 9.4 years ago • Paulo Nuin

fit <- lmFit(selDataMatrix, design) cont.matrix <- makeContrasts(FacCont=Group1-Group2, levels=design) fit2 <- contrasts.fit(fit, cont.matrix) gives an error message because the original design matrix includes...the covariates. Error in contrasts.fit(fit, contrast.matrix) : Number of rows of contrast matrix must match number of coefficients In addition: Warning messages…

updated 14.3 years ago • Belmont, John W

What does "Level 3" mean in "Level 3 TCGA tumor samples"? Are there Level 2 and Level 1 also. Please explain

TGCA

updated 5.8 years ago • omarrafiqued

Hello everyone, I analyzed RNA-seq data and I noticed that the rlog value of the reference level for some genes are lower then the rest of the samples, how can the Log2FC be negative if the reference level has lower compared

deseq2

updated 6.2 years ago • Morris

by the genome studio software. Here is the code. If you have some available time I want to you to validate the code . setwd("W:/KAUSHAL_RESEARCH/K_Surendaran/Data") source("http://www.bioconductor.org/biocLite.R") biocLite

GO GO

updated 12.2 years ago • Guest User

fit2, coef = 1, adjust = "BH", number = 50) Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type I am trying to fix this error from last few days but couldn't find a solution. I...while using the topTable from limma: > > Error in array(x, c(length(x), 1L), if (!is.null(names(x))) > list(names(x), : >…

Normalization affy limma convert Normalization affy limma convert

updated 12.7 years ago • Atul Kakrana

genes 3utr sequence. I am NOT sure about my mapping between BioMart and miRecords objects name. Clearly the output of my algorithm depends upon the correct (is it ?) names mapping. > [miR-130a] [1] "TAAACTACCTAACATTATTTATTCAGCTTCATTTGTGTCAATGGGCAATGACAGGTAAATTAAGA...ensembl_gene_id','external_gene_id','refseq_dna'. The filters I used assume that BioMart data named "hgnc_automatic_gen…

GO Homo sapiens biomaRt GO Homo sapiens biomaRt

updated 16.4 years ago • mauede@alice.it

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updated 18.9 years ago • Lana Schaffer

treating each miRNA as a 'gene'** i.e. the gene DE is essentially the same as transcript level DE. In either case, we are really counting mature miRNA *transcripts* (they do not have the same splicing or isomer variants...28 bp reads. For the purposes of this question, I have mapped the reads with Salmon (assume this is 'valid'). #### Query When using DESeq2 or edgeR or limma and tximport wit…

tximport DESeq2 edgeR swish miRNA

updated 3.4 years ago • BG

I have been trying to annotate the gene symbol for the row name of my data frame H3com using the command: H9comm$Gene_SYMPOL<- mapIds(org.Gg.eg.db, keys = rownames(H9comm), keytype = 'ENSEMBLTRANS...an error Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBLTRANS'. Please use the keys method to see a listing of valid arg…

R ensembldb Annotation

updated 3.1 years ago • Mohamed