Bioconductor Forum

nc NChannelSet (storageMode: lockedEnvironment) assayData: 1178100 features, 50 samples element names: exprs protocolData rowNames: GWAS16.10_160_CD16.CEL GWAS16.11_158_CD16.CEL ... GWAS16.L_148_CD16.CEL (50 total...m currently coercing GeneFeatureSet objects to NChannelSet and as you can see the conversion yields valid objects. As a workaround, is there an alternative class to which I sh…

updated 14.2 years ago • Tim Rayner

i.e. WT to KO). I now have one Ctrl condition and three different mutations (say Mut1, Mut2 and Mut3): levels(condition) # my 4 different conditions # [1] "Ctrl" "Mut1" "Mut2" "Mut3" dds # my DESeqDataset, including the results # class: DESeqDataSet...ENSMUSG00000000028 ... ENSMUSG00000093778 ENSMUSG00000093789 # rowData metadata column names(31): baseMean baseVar ... deviance maxCooks # colna…

Sequencing ReportingTools DESeq2 Sequencing ReportingTools DESeq2

updated 11.9 years ago • Dimitra Alexopoulou

tmp\*\`, iseq, value = c("ENSP00000469853", "ENSP00000472959",  :   invalid factor level, NA generated So, i do get some orthologues, however the majority of rows were replaced with NAs from human ENSEMBLPROT

annotation

updated 10.2 years ago • bruno.gotti

github.com/YuLab-SMU/DOSE/wiki/how-to-prepare-your-own-geneList][1] ```r geneList = DEedgeR[,2] names(geneList)= as.character(DEedgeR[,1]) #up until here it was okay #but when I ran this last part geneList = sort(geneList, decreasing...TRUE) #I got this Error in do.call("cbind", lapply(x, "is.na")) : variable names are limited to 10000 bytes ``` I don't know what's wrong since I followed the sam…

clusterProfiler

updated 5.0 years ago • Emilia

as much as we can without changing the basic features of the language. we do not want user-level code to be reliant upon details of the internal representation of objects, and the @-sign is such a detail. we want to be...to modify the internal details without breaking user-level code. this can be accomplished if we use functions to broker access to the representation. example -- X is an exprS…

updated 23.7 years ago • Vincent J. Carey, Jr.

to search I get the following: <pre> Error in normargPattern(pattern, subject) : 'pattern' must be a single string or an XString object</pre> from normargPattern (Biostrings) ciring <pre> else if (!isSingleString(pattern...stop("'", argname, "' must be a single string or an XString object")</pre>   when I test the isSingleString function, the response is …

biostrings

updated 9.6 years ago • mike_and_dan

<div class="preformatted">Hi all, I am getting a warning message when I create my contrast matrix (for a six-membered loop design experiment) that I can't find any previous threads about. The message reads: Warning message: use of NULL environment is deprecated Here is a log of how it is generated, starting with a list of my targets file: > targetsB SlideNumbe…

updated 19.9 years ago • scholz@Ag.arizona.edu

Is it statistically valid to compare biologically between two different TCGA RNAseq datasets? For instance, I want to compare between TCGA-lung

DifferentialExpression TCGAbiolinks RNASeq

updated 7 months ago • Shaimaa Gamal

strategies and packages to reduce RNAseq data from ENSEMBL gene IDs to protein coding genes with a valid NCBI.ID? I normally use the package annotables and then filter for “protein_coding” and !is.na(entrez). After that I come

annotation

updated 5.5 years ago • agustin.gonvi

0072B2", stat = "identity") 5: fastqPlot(x = fqlist\[z\]) 4: FUN(X\[\[i\]\], ...) 3: lapply(names(fqlist), function(z) fastqPlot(x = fqlist\[z\])) 2: lapply(names(fqlist), function(z) fastqPlot(x = fqlist\[z\])) 1: seeFastqPlot(fqlist) --- Output...from str(fqlist): List of 1  $ A\_bac:List of 9   ..$ fqstats: Named num \[1:3\] 10000 1560521 8 &nbs…

systempiper seeFastqPlot software error ggplot2 geom_histogram

updated 9.9 years ago • setarosd

<div class="preformatted">Hello, My name is Kevin Lee, and I am a PhD candidate in Bioinformatics at Georgia Institute of Technology. I have been trying to decide between various normalization techniques for RNA-seq methods for a parasite infection time-course study. The RNA-seq data that I will have will be from infected blood and will contain RNA from both the host and the parasite. I…

Normalization DESeq DEXSeq Normalization DESeq DEXSeq

updated 12.6 years ago • Kevin Lee

<div class="preformatted">Dear Jeremy, > Date: Wed, 23 Sep 2009 13:26:57 -0700 > From: jeremy wilson <jeremy.wilson88 at="" gmail.com=""> > Subject: [BioC] Help on contrast matrix Limma > To: bioconductor at stat.math.ethz.ch > > Hello bioconductor group, > > I am stuck with understanding how to create contrast matrix for &g…

updated 6.9 years ago • Gordon Smyth

maNspots [1] 46080 @maSub [1] TRUE TRUE TRUE TRUE TRUE 46075 more elements ... @maPlate factor(0) Levels: @maControls factor(0) Levels: @maNotes character(0) @maGnames An object of class "marrayInfo" @maLabels [1] "1" "2" "3" "4" "5" 45691 more...elements ... @maInfo Name Clone.ID X13834 13834 IMAGE:342721 X13846 13846 IMAGE:233721 X13929 13929 IMAGE:50754 X13941 13941 IMAGE:12…

updated 19.9 years ago • Wu, Zhuang

have 6 samples/ groups with 3 replicates (In total 17; one sample contains 2 replicates). the sample names are Mf, Bf, Ef, Mr, Br, and Er. I want to get DEGs (differentially expressed genes) between Mr-Mf, Br-Bf, Er-Ef. For doing that, I subsetted...colnames(design_matrix)) # To creates a contrast matrix (cm) comparing the expression levels between Mr and Mf cm <- makeContrasts(Mr…

subsettingdata edgeR designmatrix

updated 19 months ago • prity6459

I apologize for my naiveté but I'm fairly new to R and very new to limma. My overall research question is to determine whether or not there is a difference in gene expression between post-intervention and pre-intervention of a group of patients. I wanted to adjust for potential confounding covariates such as contamination of the sample from white blood cells which I had arrived at by creating two…

limma covariates

updated 9.9 years ago • trinhpauline

IFNG.24 > > > targets <- readTargets("Targets.txt") > ># build factor of target names > > targetnames <- c(rep("C.1",4), rep("C.6",4), rep("C.24",4), >rep("IFNG.1",4), rep("IFNG.6",4), rep("IFNG.24",4)) > > > targetnames <- factor...targetnames, levels=c("C.1", "C.6", "C.24", >"IFNG.1", "IFNG.…

limma limma

updated 20.3 years ago • Gordon Smyth

a dataset with both biological and technical replicates. There is 1 factor with 8 different levels, denoted A-H Biological replicates of a given level are denoted by 1,2, ... Technical replicates corresponding to a given...biological replcate are denoted 2a,2b.. I wish to compute the statistics of each of levels B-H)relative to level A. I would greatly appreciate it if someone were to look at t…

Survival cdf annotate affy limma gcrma matchprobes affyio Survival cdf annotate affy

updated 18.2 years ago • Richard Friedman

<div class="preformatted">Persons interested in peer review of Bioconductor packages please send me an e-mail with content PACKAGE [package id] REVIEWER [your name and email address] then contact the maintainer of the package you are interested in (retrieve email address from the associated...of Bioconductor packages please send me an e-mail with content PACKAGE [package id] REVIEWER […

PROcess PROcess

updated 23.7 years ago • Vincent J. Carey, Jr.

control","hydro_phos"),res = res).</pre> I confronted an error: <pre> Error in results(dds.shr, name = coefAlpha) : object 'coefAlpha' not found</pre> My codes are: <pre> setwd("C:/cygwin64/home/Coexpression_Nov2017") getwd() library

deseq2

updated 8.0 years ago • lychen83

1: /usr/local/lib/R/site- library/Biostrings/include/Biostrings_defines.h:50:2: error: unknown type name cachedCharSeq /usr/local/lib/R/site- library/Biostrings/include/Biostrings_defines.h:59:1: error: unknown type name cachedXVectorList...usr/local/lib/R/site- library/Biostrings/include/_Biostrings_stubs.c:78:1: error: unknown type name __get_cachedXStringSet_elt_funtype__ /usr/local/lib/R…

Rsamtools Rsamtools

updated 12.0 years ago • nishant thakur

fun = "enrichGO", OrgDb = "org.EcK12.eg.db",ont="BP") I get this error: Error in `levels<-`(`*tmp*`, value = as.character(levels)) : factor level [4] is duplicated

clusterProfiler Bioconductor R DEGs

updated 5.5 years ago • tpm

is my R code (i use a "Targets" csv-like file in which i write the path to the files, the sample name, and their group (there are replicates)): ```r #!/usr/bin/env Rscript library(BiocParallel) library(bsseq) sessionInfo() BiocManager...valid() targets_path <- "/path/to/Targets.txt" # Loading data targets<-read.delim( targets_path, header=TRUE, sep="\t", …

HDF5Array BiocGenerics BiocParallel Biobase

updated 20 months ago • jacques.imbert

Hello, After reading the vignette, I decided to combine factors of interest into a single group (in this case it is Age and Genotype) rather than using an interaction term. I am interested in comparing differences between genotypes at certain ages of animals. I manually edited my matrix because there are levels without samples. When I attempt to pass in my manually edited matrix with the combi…

DESeq2

updated 4.8 years ago • jd348

adapt code > written for Agilent single channel data, is how to 'automatically' > include gene names, symbols, GO IDs etc in the topTable output. While it > may be easy enough to use mget to retrieve the necessary info for...gt; so far. > > Since there is such a rich repository of data in hgu133plus2.db, there > must be a way to tap into this without goin…

GO hgu133plus2 affy limma convert Category GO hgu133plus2 affy limma convert Category

updated 14.8 years ago • Gordon Smyth

div class="preformatted">Hello, My name is Matthew Morris, I'm a second year Master's student at the University of Calgary, and I am fairly new to the world of microarrays...targets$Temperature, sep=".") #check to see it worked TS #set up design TS <- factor(TS, levels=c("Hog.7","Cran.7","LCM.7","OL.7", "Hog.23", "Cran.23", "OL.23", "LCM.23", "Hog.15")) design <- model.matri…

updated 14.2 years ago • mrjmorri@ucalgary.ca

MSc degree (of BSc degree for MS+PhD applicants) at the   Commendation/Distinction level in computer science, electrical   engineering, or mathematics. - Excellent programming skills. - Experience in machine...responsible for the actual admission offer, stipend and benefits. How to apply: Full application must be submitted through the application website at http…

job MSc PhD machine learning Job

updated 8.2 years ago • senaykafkas

to be that in order for a `` REF `` interval to overlap a `` TEST ``interval, it must cover >50% of `` TEST `` interval.  I've been playing around with GenomicRanges. However, the `` findOverlap...13468022L ), Deft = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), .Names = c("chr", "start", "…

genomicranges

updated 10.2 years ago • khauser130d

things like %in% and intersect, but no luck (I am guessing because the rows are different beyond the name. I did read the section on filtering reads (and I have already filtered low counts). But couldn't figure out how I could filter

deseq2

updated 6.3 years ago • rattray56

from GDC, but they seem to have been removed from the GDC Data Portal. When using GDCquery, the only valid argument for "workflow.type" now seems to be "STAR - Counts". Is there a way to retrieve the older version HTSeq Counts

TCGAbiolinks

updated 3.7 years ago • vm

I fail at: > rep <- getReposEntry("BIOCRel1.1") Note: BIOCRel1.1 does not seem to have a valid repository, skipping Is there something in disarray? Kind regards Reinhold Koch </div

updated 23.0 years ago • Reinhold Koch

TRUE, logical = TRUE, warn.conflicts = warn.conflicts, : 'reposTools' is not a valid package -- installed < 2.0.0? I am not knowledgeable enough to figure this out... Sincerely, Juliette</div

updated 21.1 years ago • Juliette Colinas

div class="preformatted">I just wanted to check if RNA Seq counts generated using RSEM, are a valid input for edgeR package? -- Maria Dermit Ph.D. Student, Luscombe group EMBL-European Bioinformatics Institute Wellcome

edgeR edgeR

updated 13.1 years ago • Maria Dermit

S_63 S_64 Thymus Thymus Trachea Trachea 32 Levels: Adrenal_cortex Adrenal_gland Appendix Bone_marrow ... Whole_brain Hope this helps. Please let me know if you have...Error in getMatrixFromExpressionSet(expressionMatrix, condition.factor, > : > condition must be of class factor" > > The code of the program is: > &…

Kidney Lung Prostate probe SpeCond Kidney Lung Prostate probe SpeCond

updated 12.0 years ago • Florence Cavalli

<div class="preformatted">I am currently working on the analysis of array CGH data of Glioblastoma multiforme patients, obtained from the TCGA website. The data was obtained from the Level 1 archive of CNV (CN Array) data type from the Agilent Human Genome CGH Microarray 244A platform. Initially, I created an...of Glioblastoma multiforme patients, obtained from the TCGA website. The data w…

Microarray Annotation CGH snapCGH Microarray Annotation CGH snapCGH

updated 11.3 years ago • Guest User

Since RIPSeq tends to be noisy, I need to "subtract" out any RNAs that might bind at a background level. I have read online that I cannot subtract counts but then I am not quite sure how to compare my DESeq2 results data frames...5. If so, remove gene from experimental condition list So my question is whether or not this is valid and if there is a better way to do this kind of comparison to de…

deseq2 differential expression immunoprecipitation

updated 9.4 years ago • snamjoshi87

package, when .install_n_invalid_pkgs is called. When I run install, `valist` in install (and thus `valid` in .install_n_invalid_pkgs) is just TRUE, rather than a list, as the function expects. So the problem seems to lie in the...valid() function.</p> </td> </tr> </tbody> </table> <pre> > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-p…

biocmanager installation

updated 7.2 years ago • Kyle Johnsen

I'm running analysis of a small number of samples using RNA-seq and ATAC-seq, which produce reads mapping to genes and open chromatin, respectively.  I use DESeq2 to estimate scaling factors for each sample, so that I can compare e.g. the number of reads for region _r _in sample A to region _r _in sample B.  However, several samples failed ATA…

deseq2 estimatesizefactors

updated 7.1 years ago • owenchapman1

However, the actual argument instead of "silent" seems to be "verbose" (silent is not a valid argument, and this can be checked also looking at the code) and neither "cores.ratio" nor anything like it is a valid argument

tronco

updated 9.6 years ago • Ramon Diaz-Uriarte

on the elementMetadata to be really slow, slower than it need to be I would say (I suspect some validity checking, see comment below on row subsetting). * There is no easy shortcut to get a specific metadata column (gr[, "score...function at the bottom of my email, for doing this. * Since start, end, width are reserved column names for GRanges, it would be nice if the GRanges constructor was ex…

updated 15.2 years ago • Kasper Daniel Hansen

storageMode: lockedEnvironment) > assayData: 34760 features, 6 samples > element names: exprs > protocolData > sampleNames: GSM910962.CEL GSM910963.CEL ... GSM910967.CEL (6 total) > varLabels: ScanDate...table ID <- featureNames(eset) Symbol <- getSYMBOL(ID, "mogene10sttranscriptcluster.db") Name <- as.character(lookUp(ID, "mogene10…

Microarray Annotation annotate limma ASSIGN Microarray Annotation annotate limma ASSIGN

updated 11.4 years ago • Jakub Stanislaw Nowak

extendedMapSeqlevels() for using GenomeInfoDb when there is information regarding the species and naming style of interest. Otherwise sequence names are left unchanged." - [Source](https://github.com/lcolladotor/derfinder/commit...9739f1242d74315a2ce5e91acc63a74911964caa).   Reading, "otherwise sequence names are left unchanged", I thought rather than take the time to figure out how to …

derfinder GenomeInfoDb GenomicRanges

updated 8.6 years ago • Wayne

s not allowed if 'na.rm' is FALSE") 5: quantile.default(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, names = FALSE) 4: quantile(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, names = FALSE) 3: diff(quantile(as.numeric(x), c(0.25, 0.75), na.rm = na.rm...names = FALSE)) 2: FUN(newX[, i], ...) 1: apply(exprs(d.norm), 1, IQR) > qDE.ttest <- ttestCtData(sr.norm[,1:4], groups=…

Clustering Cancer PROcess cycle HTqPCR Clustering Cancer PROcess cycle HTqPCR

updated 15.5 years ago • deepak roshan

<div class="preformatted">Dear Stephanie, > Date: 30 April 2014 > From: Pekka Kohonen <pkpekka at="" gmail.com=""> > From: Stefanie Busch <stefanie.busch2 at="" web.de=""> > To: Bioconductor <bioconductor at="" r-project.org=""> > Subject: Re: [BioC] 1. comparing chip Information in meta analysis / Rankprod and 2. two color normalization…

Normalization probe limma RankProd Normalization probe limma RankProd

updated 11.6 years ago • Gordon Smyth

function for use with Gviz::AlignmentsTrack. It will import a bamfile # with non-UCSC chromosome names (i.e. "chr7" instead of just "7"). importFunctionNonUCSC <- function (file, selection) { indNames <- c(sub("\\.bam$", ".bai", file), paste(file...scanBamFlag(isUnmappedQuery = FALSE)) reads <- if (as.character(seqnames(selection)[1]) %in% names(Rsamtools::scanBamHead…

gviz biostrings

updated 9.0 years ago • stianlagstad

versions of these questions asked before on this forum - but would like to ask additional questions namely regarding the normalization procedures. (see: [https://support.bioconductor.org/p/116282/][1] and [https://support.bioconductor.org...sites is the same and the sites are almost all the same as well. My question is simple, is this a valid approach to this problem? Or should more time be…

csaw ChIPseq DESeq2 DiffBind

updated 8 months ago • Luca

Best, Leo --- <img src="https://pbs.twimg.com/media/ER7OOKXXYAk_ycI?format=jpg&name=4096x4096" width="600px"/> 🔥off the press! Check 👀 our @biorxivpreprint on human 🧠brain @LieberInstitute spatial 🗺️🔬transcriptomics...shiny web app * Assessment of known markers * Identification of layer-specific markers * smFISH validation ✅ * spatial registration of snRNA-seq data …

biorxiv spatialLIBD News

updated 5.8 years ago • Leonardo Collado Torres

checkDataset(dataset = dataset, mart = mart) : The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function.</pre> If I run the same line calling useMart or useDataset

software error biomart usemart usedataset

updated 8.0 years ago • lpsantamaria

first base of the reads if 'G' and not aligned to the genome... Error in checkSlotAssignment(object, name, value) : assignment of an object of class "IRanges" is not valid for slot 'ranges' in an object of class "GPos"; is(value, "IPos") is not

cager

updated 7.2 years ago • Pengcheng Yang

5_utr_start","5_utr_end" + ) > all(att%in%martAttr[,1]) #valid names for the mart [1] TRUE #works fine here > tempGene <- getBM(att,filter="ensembl_gene_id",value="ENSG00000187634",mart

biomaRt biomaRt

updated 16.9 years ago • Elizabeth Purdom

the filetable or the filenames ``` The IDs are on the compound list as well as on the mzML files name (separated with _ ). When loading the list, I have no problems: ``` > loadList("./PFAS_list.csv") Loaded compoundlist successfully...issue. ``` I re-installed BiocManager but did not managed to check mzR: ``` > BiocManager::valid() [1] TRUE > library(BiocManager) …

software error RMassBank

updated 5.8 years ago • jean.froment

I assume this is because it is whats available without having to build the Eset themselves. Is this valid, has anyone else tried

MineICA

updated 9.4 years ago • sgore83

that this was proportional to the rate on the other arrays. It also made me further question the validity of the MAS5 calls. Comments from the mailing list (and a published reference that I could show the reviewers) would...PAcalls@exprs) > ># Get those probesets with at least 1 present call >my.list <- names(np[np>0]) > >The simpleaffy library a…

affy gcrma simpleaffy affy gcrma simpleaffy

updated 20.9 years ago • Naomi Altman

_data) exprSet.nologs <- exprs(eset\_rma) head(exprSet.nologs) \# List the column (chip) names colnames(exprSet.nologs) \#log transformation exprSet = log(exprSet.nologs, 2) head(exprSet) \#To print out our expression...5),rep("Pediatric",5))) groups design\_new<-model.matrix(~0+groups) colnames(design\_new)=levels(groups) design\_new fit&l…

limma

updated 7.9 years ago • lawarde.ankita1

<div class="preformatted">Dear Limma users, I'm currently working on Affymetrix microarray (Hu-gene 2.1) with only one channel. I got 8 experimental stimuli conducted on 7 donors. During the experimental process each stimulus was conducted at the same time for all the donors so I assume there are no technical replicates, but I need to take in account the "donor effect" (or biological repli…

Microarray limma PROcess Microarray limma PROcess

updated 11.8 years ago • Santy Marques-Ladeira

<div class="preformatted"> This may be a very basic question, but I am looking in the R manual and I haven't found the right function... and I am sure it must exist already. So I apologise in advance if I seem to be blind or missing something! :) What I am after is very simple. I am using Limma and I have a number of data frames (RGList, MAList, MArrayLM...). Sometimes I just want to locat…

limma limma

updated 19.6 years ago • J.delasHeras@ed.ac.uk

because of correction and other english errors. WHAT WE EXPECT FROM A CANDIDATE: - Applicants must be living in USA,Canada, Australia or United Kingdom. - Applicants must be high school or vocational high school graduates...Above 18 years old. - Confident computer skills. - Applicants must be avaliable to check his/her e-mail messages between 7am - 12noon. - Good working rela…

updated 17.8 years ago • Storistes de France

index.php?ref=HD_00995 </a></td> </tr> </tbody> </table> ##   ## Job Description A PhD-level research staff position is available to head the EMBL Centre of Biological Modelling (CBM) based at EMBL’s Heidelberg

exciting job modelling Job

updated 9.0 years ago • Wolfgang Huber

vjust = -1.5, size = 3) </pre> However I get the error <pre> Error in .local(data, ...) : label must be one of column names</pre> This error doesn't appear if I revert to the previous version of ggplot2, keeping the same version...of ggbio. Any particular workaround? I tried to put the names as metadata to the GRanges object and use the "column" name as label, but didn'…

ggbio ggplot2

updated 7.2 years ago • Lescai, Francesco

Sm149Di Sm152Di Sm154Di Tb159Di Tm169Di Yb170Di Yb171Di Yb172Di Yb173Di Yb174Di Yb176Di Time \#add names to the list of flow frames names(frames) <- sapply(frames, keyword, "SAMPLE ID") fs<-as(frames,"flowSet") \#ERROR Error: Replacement...nbsp;   1 obs. of  1 variable:   .. .. .. ..$ labelDescription: chr "Name"   .. .. ..@ da…

flowCore flowcore CyToF Rtsne

updated 10.3 years ago • clevy

gene.hobj, >hopach.arrays = NULL, dist.genes= gene.dist, gene.names= NULL) GENE TREE: Working on level 16 Working on level 15 Working on level 14 Working on level 13 Working on level 12 Working on level 11 Working on level...10 Working on level 9 Working on level 8 Working on level 7 Working on level 6 Working on level 5 Working on level 4 Working on level 3 Working...on level 2 Working on…

hopach hopach

updated 20.7 years ago • Anthony Bosco