Bioconductor Forum

pre> DESeqDataSet(se, design = ~ condition)</pre> Where "condition" is the actual column name. I'd like to have the column name be adjustable. I tried using a variable in the formula: <pre> design_col = "condition" DESeqDataSet...design_col)</pre> As might be expected, that does not work ("all variables in design formula must be columns in colData"). I then tri…

deseq2 r design matrix

updated 9.3 years ago • igor

div class="preformatted">Hi everyone: We need bead level data (not bead summary data) from Illumina Sentrix Whole Genome Expression BeadChips (Human version 2 or 3, or mouse version...there is any such data available on the Internet, or can we share with your data if you have? Bead level data are obtained by changing the setting of Illumina BeadScan to allow it to output intensity for eac…

Normalization Normalization

updated 16.9 years ago • Wei Shi

TRUE, plotDendrograms=FALSE) I tried colorLabels=FALSE and nothing changed. I tried ySymbols=names(MEs) which gave an error that the number of ySymbols must match the number of rows in the adjacency matrix. I tried to figure

R WGCNA

updated 6.1 years ago • normingt

but I got an error report Error in stop_if_wrong_length("'seqnames'", ans_len) : 'seqnames' must have the length of the object to construct (1) or length 1 here is my code library(BayesPeak) rm(list=ls()) options(stringsAsFactors

Guitar

updated 3.8 years ago • 建国

Hi everyone, I'm trying to use CHIPseeker for CutnTag data, and had a question regarding getting the names of each annotation. I've used annotatePeak to get an idea about the promoter, exon and intergenic region, but is there a...everyone, I'm trying to use CHIPseeker for CutnTag data, and had a question regarding getting the names of each annotation. I've used annotatePeak to get an idea a…

ChIPseeker CHIPsee

updated 4.5 years ago • rithika.behera

<div class="preformatted">Centre Nationale de la Recherche Scientifique Lille (France) Bio-statistiques The laboratory of Genetics of Multi-factorial Diseases (CNRS/University Lille 2), located in the Lille Biology Institute (Lille, FRANCE) is an active research group in Genetics Epidemiology of Obesity and Type 2 Diabetes. We are conducting genetic linkage and geneti…

Genetics Genetics

updated 20.0 years ago • Sophie Gallina

files are ( mine or GEO one that had worked fine), now I always see an error as "All the CEL files must be of the same type. Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not TRUE".... So I'm wondering if anyone has...cell files", full.names = TRUE) > affyGeneFS <- read.celfiles(geneCELs) All the CEL files must be of the same type. Error: checkChipTypes(filenam…

BiocViews Annotation Organism biocViews oligo BiocViews BiocViews Annotation Organism

updated 14.5 years ago • Setsuko Sahara

res <- nbinomTest( cds, "N", "T" ) I get numbers under ids because on page 4 we removed the gene names. countsTable <- countsTable[ , -1 ] How can i get my res to match what is in the manual with gene names under id? Thanks, Mary Ann

DESeq DESeq

updated 14.0 years ago • Mary Ann Allen

Hi All, I have performed a differential expression analysis using DESeq2, and would now like to analyze enriched GO terms using the topGO package.  However, I am having difficulty formatting the gene names for input.  Here's what I have so far. <pre> ## create named vector of p values GO_genes = setNames(res$padj, row.names(res)) ## create a gene selection function …

topgo biomart deseq2 gene ontology

updated 8.6 years ago • krc3004

one. I have used Rnbeads to generate M values for some 450k arrays, can happily export the site level data by cg ID and gene/promoter level data too. However, I can't find a simple within R way of generating a list of cg IDs by

MethylationArrayData RnBeads

updated 4.8 years ago • D

on GEO. Does anyone have any tips or BioConductor libraries that can generate gene expression levels from TSV files on GEO ? I have been filtering GEO series records with the following query ("tsv"[Supplementary Files]) Thank

GEOquery GEO TSV

updated 17 months ago • gallantk5

proFIAset(path, ppm=ppm, parallel=FALSE) Error message: Error in (function (cl, name, valueClass) : assignment of an object of class “logical” is not valid for @‘noiseEstimation’ in an object of class “proFIAset

software error proFIA HRMS FIA Metabolomics

updated 5.6 years ago • Esther G.

dataset, mart = mart) :    The given dataset:  hsapiens\_gene\_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function. Then I tried load a different dataset, still

biomart

updated 8.0 years ago • shenwei1376

using `STAR`, and got `ReadsPerGene.out.tab` outputs. I am trying to use `tximport` to build a gene-level count matrix for DESeq2 analysis using the STAR outputs. Yet I haven't been able to find a way to do it. I have checked the...I am wondering if anyone has suggestions on how to use tximport and STAR outputs to make a gene-level count matrix? Thanks, Bo

STAR tximport RNASeq DESeq2

updated 24 months ago • Bo

sex) <span style="background-color:Yellow"><strong>Error in seq_len(length(idx) - 1) : argument must be coercible to non-negative integer </strong></span>In addition: Warning message: In DESeqDataSet(se, design = design, ignoreRank...sex) <span style="background-color:yellow"><strong>Error in seq_len(length(idx) - 1) : argument must be coercible to …

DESeqDataSet DESeqDataSetFromMatrix rnaseq deseq2

updated 9.4 years ago • ErickF

nbsp;contains more information than the species and genus, that will not be used in the package name. For example, I create a TxDb object: <pre> url <- "http://plasmodb.org/common/downloads/Current_Release/PbergheiANKA/gff...Genetics, TxDb, Plasmodium_berghei_ANKA </pre> So, is there a way to make the package name be `` TxDb.PbergheiANKA `` when creating it with `` makeTxDb…

genomicfeatures txdb

updated 10.5 years ago • Diego Diez

the export method in rtracklayer for the GRanges class requires that the GRanges object have unique names. The error message given when names are not unique is the following: Error in export(object, FileForFormat(con), ...) : cannot...export object of class 'GRanges' As one can easily make a case that non-unique names may be troublesome, I am curious to know whether you intentionally disall…

rtracklayer rtracklayer

updated 12.9 years ago • Samuel Younkin

div class="preformatted">Hi, I was trying to map gene symbols to gene names using the org.Hs.eg.db package. I first convert the gene symbol to an entrez id, and then convert that to a gene name (example...code below). However, during this process I can't get the gene names for some of the genes: -------------------------- library(org.Hs.eg.db) ### First two genes are ok... symbols <…

convert convert

updated 11.6 years ago • Tim Smith

<div class="preformatted">Hi, I'm creating my limma design matrices by hand and am just wondering whether the sample names in the matrix actually matter or whether they may be arbitrary as long as they reflect the ascending order of array columns...Hi, I'm creating my limma design matrices by hand and am just wondering whether the sample names in the matrix actually matter or whether they…

limma limma

updated 16.1 years ago • koechert, karl

Hello everyone, I have a problem with creating OMICS object in my analysis. After downloading a TCGA data for glioblastoma I have tried crating OMICS object but unfortunately I stumbled upon a problem. Downloaded data from TCGA includes access number and not symbol of the gene. ```r library(pathwayPCA) library(TCGAbiolinks) library(tidyverse) library(SummarizedExperiment) query…

pathwayPCA TCGAbiolinks TCGAbiolinksGUI.data

updated 3.1 years ago • Mikołaj Mierzejewski

tmp, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels Again I modified the above command. The command is results_transcripts = stattest(bg_chrX_filt,feature= c("gene","exon...tmp*, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels In addition: Warning message: In stattest(bg_chrX_filt,…

software error ballgown rstudio R stattest

updated 6.6 years ago • fatimarasool135

Hi all, I've just started using flowsom and ive run into a few issues: 1. flowsom takes direct input of the fcs files but wont take a flowset directly  fs<-read.flowSet(jfiles.out) > fs A flowSet with 8 experiments. fs=ReadInput(fset) Error in ReadInput(fset) : Inputs of type list are not supported.          &…

flowcore flowsom

updated 9.3 years ago • jeremyeadler

Hi, Can we change the name of the ColAttributes in the image generated by dba.plotHeatmap? As I have two attributes in my data `DBA_CONDITION`, `DBA_FACTOR...but want to name "Factors" as "Histone Mark" in the figure generated by `plot()` or `dba.plotHeatmap()`. Is it possible to do so? Thanks

DiffBind plot plotHeatmap dba.plotHeatmap

updated 6.3 years ago • researcher

MSAvsCTRL\_FCTX = fMSA\_FCTX-fCTRL\_FCTX,   MSAvsCTRL\_CRBL = fMSA\_CRBL-fCTRL\_CRBL,   levels=design) fit2 <- contrasts.fit(fit, cm) fit2 <- eBayes(fit2)   To answer the other questions I need to use multi-level...pd$Group,myLoad$pd$Region,sep=".")) design1 <- model.matrix(~0+regions) colnames(design1) <- levels(regions) corfit &…

limma epic methylation limma design matrix covariates

updated 7.2 years ago • c.bettencourt

We have created a new experimental data package called 'seqc'. It includes gene-level read count data generated by the SEQC (SEquencing Quality Control) project, which is the third stage of the well-known...bioconductor.org/packages/release/bioc/html/Rsubread.html) program. This package includes the gene-level read count data for 2,758 libraries. It can be downloaded from the following link (188M…

seqc rsubread featurecounts subjunc ercc News

updated 11.0 years ago • Wei Shi

the XML package. Internally you can access, modify, merge and do some other stuff and if it's still valid BioPAX it can be exported into .owl again. There are alot of convenience function available, see the manual for a complete...graphs) into graphs, and can be visualized with Rgraphviz. Parsing is currently restricted to Biopax Level 2, but Im working on integrating Level 3 already. There is q…

Pathways Network Rgraphviz rBiopaxParser Pathways Network Rgraphviz rBiopaxParser

updated 13.2 years ago • Frank Kramer

NIPTeR is experiencing new warnings when loading Biostrings. I have the exact same warnings with my package, CNVScope. I would post sessionInfo(), but this occurs only on the check debian servers. It doesn't happen on windows 10 or Ubuntu (zero problems there). I realize that one response will probably be to ask it of someone else associated with CRAN (perfectly valid to ask), but I'm wonderin…

Biostrings

updated 6.0 years ago • james.dalgleish

B 3 C 1 C 2 C 3 > batch [1] A A A B B B C C C Levels: A B C > treatment [1] 1 2 3 1 2 3 1 2 3 Levels: 1 2 3 ``` I would like to determine all of the pairwise differences between the three...treatments while controlling for batch. There is no "control/baseline" level for either `batch` or `treatment` here, so there is no clea…

deseq2 differential expression batch correction design

updated 6.5 years ago • wunderl

<div class="preformatted">Hi, I'm trying to take a list of genes and their attributes (e.g. exon count) and get average exon count for genes in the different top level GO categories (1 step below the MF, BP and CC top domain). After reading the maillists, vignettes and googling around I'm still...and their attributes (e.g. exon count) and get average exon count for genes in the different …

GO graph biomaRt GO graph biomaRt

updated 18.3 years ago • Palle Villesen BiRC

lt;- BiomartGeneRegionTrack(genome = "hg19", chromosome = chr, start = 20000000, end = 21000000, name = "ENSEMBL") Fehler in getBM(attributes, filters = filterNames, values = filterValues, : Invalid attribute(s): external_gene_id...Please use the function 'listAttributes' to get valid attribute names</pre>   __How should a BiomartGeneRegionTrack be called?__ This also pro…

gviz biomart

updated 10.7 years ago • tonja.r

div class="preformatted">Hello, I used RSEM to extract gene and transcript level read count information for our single end read libraries. Then rounded off the expected read counts to use for differential...expression analysis using edgeR at both transcript and gene level. However, I found that the number of DE transcripts were almost 10 times less than those of genes. Is this expected or s…

edgeR edgeR

updated 12.3 years ago • Alan Smith

showed significant differences in our previous experiments using different material. The complete name of the pathway after the analysis is "AGE-RAGE-signaling pathway in diabetic complications" (https://www.genome.jp/pathway...activate AGE-RAGE signaling) and that is why I ask myself if it is accepted to shorten the pathway name to "AGE-RAGE-signaling pathway"? On Wikipathway for example, you ca…

pathways Pathways

updated 2.8 years ago • Katharina

geni, "genesUC.html", mapURL = SMDclid) : Object "SMDclid" not found SMDclid wasn't a valid option ? How and where can I link CloneIDs ? (BTW I'm just discovering that widget.mapGeneInfo it doesn't work anymore... it...gives Error in widget.mapGeneInfo(names) : couldn't find function "widgetRender" thanks a lot Giulio > </div

updated 20.5 years ago • Giulio Di Giovanni

I was faced with the following error message. Normalizing Data Error in checkSlotAssignment(object, name, value) : Value supplied is not valid for slot "pm", is(value, "matrix") is not TRUE To make sure the cel,cdf files are loaded properly

cdf convert cdf convert

updated 23.1 years ago • Sundaram, Shyam NIH/CIT

Hi, I have a question regarding limma-driven microarray analysis. I have a total of 24 arrays. My experimental design consists in two fixed factors, i.e. "matrix" (F or G) and "dim" (2 or 3), and what I consider a Random Factor, i.e. "donor". There are six donors, so that each donor has provided a matrix * dim treatment. That is: 4 possible combinations matrix * dim * 6 donors = 24 arrays.…

limma multi-level random effect

updated 6.6 years ago • David Rengel

Hi,   I hope you are having a good time. My name is Taha ValizadehAslani. I am a graduate student at EESI lab Drexel University. We are interested in your software package...Anaconda2/envs/mro\_env/lib/R/library/r2d3' In R CMD INSTALL When I try BiocManager::valid()  I get the following messaage: \* sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86\_…

signer install error

updated 7.0 years ago • taha.valizadeh

and in collaboration with the R&D oncodiagnostics and oncogenomics services you: -Develop and validate mathematical and statistical algorithms for the analysis of DNA microarray data -Develop and validate normalization...for expression data -Apply biostatistical tests to determine experimental protocols for model validation -Perform analyses within the framework of the R&D and On…

Microarray Normalization Cancer Microarray Normalization Cancer

updated 19.1 years ago • Tagett Rebecca

sampleTable, directory = "./HTSeq_Output_files/", design= ~ genotype + age + genotype:age) #Re-level the data set defining G and 8dpp as the base levels ddsHTseq$genotype <- relevel(ddsHTseq$genotype,"Gy 14") ddsHTseq$age...for HTseq-count by summing exon lengths and calculating the median of transcripts per gene. Is this valid for GOseq? <pre> txdb <- makeTxDbFromGFF("..…

deseq2 goseq htseqcounts rnaseq plant

updated 9.5 years ago • Ben Mansfeld

div class="preformatted">Hi eveyone, my name is Priscila, and I'm beginning to use Limma package to analyse my microarray data. Could someone help me? I can't even start...I can't read my file Targets.txt using the Limma package. I don't know which information this file must contains, except for the .gpr file. Does anyone have a model? Thanks! Priscila [[alternative HTML version de…

limma limma

updated 17.0 years ago • Priscila Grynberg

Hello, Sorry for that very basic question: I have raw RNA-seq count data. The row names are genes, the column names are short sequences (e.g., AAACCTGCAATCTACG.1). Aren't these supposed to be sample names? What...is the name of such a file format? (Couldn't find anything online, though don't know what I have to search for.) The ultimate goal is to have

RNASeq

updated 4.3 years ago • Anne

So I have a group project where we must take RNAseq data and analyze it ourselves. We decided to use limma in order to do so, but are having some trouble understanding...meta$Carbon) > print(Carbon) [1] CH4 CH4 CH4 CH4 CH4 CH4 MeOH MeOH MeOH MeOH MeOH MeOH Levels: CH4 MeOH > Nitrogen <- as.factor(meta$Nitrogen) > print(Nitrogen) [1] NMS NMS NMS AMS AMS AM…

limma designmatrix

updated 20 months ago • avery

data that are available in the form of a matrix with Salmon quantifications summarized at gene level (non-integer values). Can they be used as an input for DESeq, and what would be the best way to do this? I am providing a sample

DESeq2

updated 4.5 years ago • luca.s

question properly. What I really meant is to compare : > >>> > >>> "Factor A level 1" vs "Factor A level 2" within "Fact B level 1" > >>> "Factor A level 1" vs "Factor A level 2" within "Fact B level 2" > >> > &gt...in the results of DESeq2 analysis really mean for the inte…

Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2

updated 11.4 years ago • Shucong Li

and technical replicates for some of them. All I need to do is a linear regression of the expression levels against time and find the slope of that line. So far so easy, but the problem I've run into is that each yeast gene deletion...So, is there any trick in limma (or in the preprocessing step prior to limma) for combining probe level data (i.e. rows of the expression matrix)? I could just ave…

Microarray Preprocessing Regression Yeast probe affy limma Microarray Preprocessing Yeast

updated 17.1 years ago • Alex Gutteridge

addGeneIDs(tss_annotated_Peaks, "org.Sc.sgd.db", c("symbol", "genename")) Error: Annotation database must be *.eg.db I can't find any hits on google with anyone else trying to do this. Can anybody make any suggestions? I can see that...the source for addGeneIDs does indeed require the name of the database to be *.eg.db. Is org.Sc.sgd.db simply not in a correct format, and therefore deliberately …

Annotation PROcess Annotation PROcess

updated 13.3 years ago • Susan Wilson

AllVariants()) Error in .mk_isActiveSeqReplacementValue(x, value) : the names of the supplied 'isActiveSeq' must match the names of the current 'isActiveSeq' unlist(mget(vars$GENEID, org.Hs.egSYMBOL

SNP annotate SNP annotate

updated 12.7 years ago • Fabrice Tourre

microarrays to do analysis. It includes 2 factors: 1week old and 5week old as ageing factors (two level) , and 4_levels genotype (yw, GMH5xyw, GMH5xFOXO,GMH5x4EBP) I assume the matrix is 1week 5week yw b0 b0+b(Ageing) GMH5xyw b0

limma limma

updated 14.1 years ago • Zhi Zhang

div class="preformatted">Hello, I am trying to use BioConductor's affy package, but there must be something wrong with the way we have things configured. We are running Solaris8 with R-1.6.1 and I have tried the following...cd CELFILES R > library(affy) Error in library(affy) : This is not a valid package -- no DESCRIPTION exists ===================================================== …

ROC reposTools affy ROC reposTools affy

updated 22.9 years ago • Susan J. Miller

I have downloaded RNA\_Seq files for mRNAs in level 3 format from TCGA database. These files contain "read\_counts". Now, my supervisor emphasizes to do quality control steps

rna-seq GC-Content qualitycontrol

updated 10.1 years ago • NS

I have a bunch of Reactome ID that I'd like to annotate with Reactome pathway names. Is there a way to do this through `` biomaRt ``? If not, is `` reactome.db `` my best option? I found this in the package manual: _Mappings

biomart reactome reactome.db id

updated 10.0 years ago • enricoferrero

is this plot function: plotMA3by2 It's great. But it doesn't seem to allow me to assign a file name. And it ignores any jpeg or other device calls before it where i could assign a filename. It is writing to the current directory

limma ASSIGN limma ASSIGN

updated 6.9 years ago • Guoneng Zhong

span style="background-color:rgb(255, 248, 220)">rownames( counts ) <- raw.data\[ , 1 \] \# gene names </span> <span style="background-color:rgb(255, 248, 220)">colnames( counts ) <- paste(c(rep("C\_R",4),rep("T\_R",3)),c(1:4,1:3),sep="") \# sample names </span...248, 220)">, value = value) : invalid 'row.names' length In addition: Warning message: Setting row …

edger tibble

updated 8.3 years ago • jattnicole29

and to make heatmaps. However, I can't figure out how to label the rows in the heatmap with gene names as opposed to ensembl IDs. I've tried to add gene names/hgnc symbols to the rlog transform values using bioMart, but I was...255)) Is there an easy way to do this. I would greatly appreciate any advice on how to get the gene names onto the heatmaps. Thanks

deseq2 gplot

updated 10.7 years ago • alchemist4au

Ringo and Starr vignette. For example, users should use: Sc:Oct_2003;chr1 to name chromosome 1 in their genome annotation file. Maybe the chr1 naming convention is specific to Nimblgen. 2. Creating the...genome Annotation object with BioMart is a good suggestion, but several things must also be matched up to get the genomeAnno object to look like …

Annotation biomaRt Ringo Annotation biomaRt Ringo

updated 16.0 years ago • Noah Dowell

I created a vector of the gene accession numbers genes <- res_log2FC$row genes <- factor(genes, levels=genes) 1765 Levels: FBgn0000356 FBgn0052644 FBgn0031621 FBgn0000644 ... FBgn0036600 gene_names<-as.factor(res_log2FC...name) # a vector containing the gene names that I assigned to the accession numbers, but the problem is that there are several...it is very very long) : ![…

DESeq2 heatmaps

updated 6 months ago • caroline.zanchi

Hello, I'm following the RNA-seq workflow : gene-level exploratory analysis and differential expression. in this step, the error appear, <pre> > library("GenomicFeatures...Hello, I'm following the RNA-seq workflow : gene-level exploratory analysis and differential expression. in this step, the error appear, <pre> > library("GenomicFeatures")…

rnaseq

updated 10.4 years ago • zhangxiaoping403

p/283372/)), and to further process them with DESeq2. My objective is to incorporate expression levels of two genes into a linear model to find significant predictors of mutation type and number in TCGA-SKCM tumours. So...tumours vs. normals, I just have a bunch of tumours). I only want to find a value for the expression level of the two genes I am interested in (find out whether there's tumours…

deseq2 tcga

updated 8.0 years ago • robles.daniela

having problems with the sampleNames for my CEL files. I have already tried to indicate the sample names in ReadAffy function but it does not help: > nm<-c("sampleA","sampleB","sampleC") > data.test<-ReadAffy(widget=TRUE,sampleNames

updated 21.6 years ago • Vitalina Komashko

I've gotten base-level DERfinder to work with smaller groups ~12 BAM files, but when i try on our larger experiment ~500 BAM files I'm running into...now there are 138394717 rows. Meaning that 0 percent was filtered. extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo\_sapiens 2017-03-15 12:20:22 filterData: originally there were 138394717 rows...2017-03-15 12:46:…

derfinder

updated 8.7 years ago • andrewelamb

I was trying to track in the web but I found nothing. Error in checkSlotAssignment(object, name, value) : assignment of an object of class "CompressedGRangesList" is not valid for slot 'rowRanges' in an object of class "DESeqDataSet

deseq2 DESeqDataSet

updated 6.7 years ago • colaneri