Bioconductor Forum

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updated 18.4 years ago • Floy

genes<-data.frame(siggenes.mrna$Gene.Name) > genes$expr<-siggenes.mrna$Score.d. > > names(genes)<-c("genes", "expr") > names(mirnas)<-c("mirna", "expr") > > dim(genes) [1] 87 2 > dim(mirnas) [1] 10 2 > genes[1:5,] genes expr 1 10386996...in RmiR(genes = genes, mirna = mirna, annotation = annota…

miRNA Annotation RmiR miRNA Annotation RmiR

updated 14.9 years ago • Mary Putt

connection made, file length 189222 bytes > opened URL > downloaded 184 Kb > > Error in names(x) <- value : > 'names' attribute [47] must be the same length as the vector [1] > In addition: Warning message: > closing unused

GEOquery GEOquery

updated 15.2 years ago • Sean Davis

pattern="FJ.wsp",full = TRUE)<br/> ws <- openWorkspace(wsfile)<br/> gs <- parseWorkspace(ws, name=1, isNcdf = TRUE)</code> But I get an error during parseWorkspace: <pre> loading data: E:/17cy1713_TSK_96wellSet/TestFiles/G1.fcs...nbsp; FL03-A not found in flowData!</pre> If I load in one of these files and check parameter names like this below, I…

opencyto flowcore flow cytometry

updated 7.2 years ago • Andrew Box

fNames=rep(c("g1","g2","g3","g4","g5"),4) fLoc=sort(rep(c("pos1","pos2"),10)) fData=data.frame(name=fNames, location=fLoc) fDatalbl=data.frame(labelDescription=c("Name of Gene", "Location of Gene"), row.names=colnames(fData...gt; data ExpressionSet (storageMode: lockedEnvironment) assayData: 20 features, 5 samples element names: exprs phenoData rowNames: a, b, ..., e (5 total) varLabels …

ExpressionData ExpressionData

updated 18.4 years ago • Kocherginsky, Masha [BSD] - HSD

Hello! I am hoping to clarify the generation of results tables for analyses using a user-generated matrices, specifically the use of the contrasts argument. My design, which features two groups at two time points and adjusts for individual, is at the bottom of this post in case it helps. What does submitting a name from `resultsNames()` to the contrast argument in `results()` give you in the co…

DESeq2

updated 5.0 years ago • thadryan

Dear limma team, although similar posts, I would need a further understanding of the “Multi-level Experiments” setting with limma.  My experiment design includes paired samples and two factors (Condition and...Dear limma team, although similar posts, I would need a further understanding of the “Multi-level Experiments” setting with limma.  My experiment design includes paired …

limma design and contrast matrix differential gene expression regression

updated 8.4 years ago • luca.piacentini

<div class="preformatted">I am trying to process the raw data downloaded from: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-380 At the moment of using the function neqc I get the following error: Error in if (sigma <= 0) stop("sigma must be positive") : missing value where TRUE/FALSE needed The problem seems to be in this line: In sqrt(weighted.mean(v, freq) * n/(n...of…

PROcess PROcess

updated 13.0 years ago • Michele

PROcess PROcess

updated 12.9 years ago • Michele

compress=FALSE)</pre> The problem is that I have many other organisms for which I must do the same. __OBJECTIVE__ How can I automate the export process in a way that the filename of the output matches the object...Scerevisiae$chrVII `` is exported, I want to see __Scerevisiae\_chrVII.fasta__ for the name of the FASTA file. __WHAT I HAVE TRIED AND HAS NOT WORKED__ <…

bsgenome biocgenerics bsapply export

updated 7.8 years ago • ረ

it returns Error in buildNodeList(graph, nodeAttrs, subGList, attrs$node) : the character vector must have names I am stuck... What have I left out Thank you Loren Engrav Univ Wash Seattle </div

GO graph Rgraphviz GO graph Rgraphviz

updated 18.0 years ago • Loren Engrav

<div class="preformatted">Hi Sam, I need to add a more informative error message - the problem is that no valid BAF values are reaching the call to CNA (baf.dat is NULL). This could happen if the values of snp.ids or chrom.ids are invalid - these should all be integer values matching the contents of snpID and chromosome in the netCDF file. What values are you using for these arguments? …

SNP cdf GWASTools SNP cdf GWASTools

updated 12.5 years ago • Stephanie M. Gogarten

Error in getBranchpointSequence(query, uniqueId = uniqueId, queryType = queryType, : Chromosome names of query and genome do not match > head(BSgenome,100) 1 function (organism, common_name, genome, provider, provider_version...lt;- character(0) 18 multiple_sequences <- RdaCollection(seqs_dirpath, mseqnames) 19 names(user_seqnames) <- user_seqnames &lt…

branchpointer

updated 3.8 years ago • alexandre.maucuer

Dear community, I am trying to perform a differential abundance analysis on 16S data using DESeq2. **The metadata is as follow** : "Prelevement" : 2 types (P1, P2) "Extraction" : 3 types (E1, E2, E3) "NS" : Corresponds to donnor ID. Each donnor (10) had 6 samples, one for each case (P1 x E1, P1 x E2, P1 x E3, P2 x E1, P2 x E2, P2 x E3) **Thus design should be** : Ext…

deseq2

updated 6.5 years ago • erwan.scaon

<div class="preformatted">Hi Cl?mentine, The "db" just adds a ".db" suffix to load the library. Just try paste(yourDb, "db", sep="."). This will give "yourDb.db". Maybe a short example will help. There is a list of 8 probesets from tha affy rat 230 2.0 array. I'm looking which of these transcripts are involved in the KEGG pathways 04710 (circadian rhythm) and 00240 (Pyrimidine metabolism):…

Annotation Pathways GO rat2302 probe affy Category Annotation Pathways GO rat2302 probe

updated 15.1 years ago • Mike Walter

<div class="preformatted">Tophat2 cmd: tophat2 -o path/to --transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensem bl/NCBIM37/Annotation/Genes/genes /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bo wtie2Index/genome 001.fastq.gz Cufflinks cmd: cufflinks --output-dir path/to --GTF-guide /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotati…

updated 11.7 years ago • Sindre

character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, : 'hexbin' is not a valid package -- installed < 2.0.0? > I found the link of hexbin 1.1-4 in the previous post message and still got same problem...Would someone tell me how to get the valid hexbin package for R 2.0.0? Thanks a lot! Yanqin __________________________________________________ …

hexbin marray hexbin marray

updated 21.0 years ago • Yanqin Yang

div class="preformatted">Hi Eric, You have NA in your name column. One fix for you without creating a name column is to just use the following code to create RangedData from your...Iranges(start=as.numeric(as.character(TwoLplus[,2])), end=as.numeric( as.character(TwoLplus[,3])),names=paste(TwoLplus[,1], TwoLplus[,2], TwoLplus[,3])), space= as.character(TwoLplus[,1]), strand= as.character(TwoL…

updated 15.8 years ago • Julie Zhu

extracting results are given below. There are 12 animals, and each animal is measured at both levels of group. Three different animals are measured within each time period. After reading vignettes and posts on designs...EXTRACTING RESULTS FOR MAIN EFFECTS AND INTERACTION IP VS IN AT EACH TIME POINT ``` results(dds, name="group_IP_vs_IN", test="Wald") #IP vs IN for dpi naive (the mai…

deseq2 Paired Nested

updated 5.9 years ago • julia.chariker

<div class="preformatted">Hello everybody, I am using the hclust() function in R. I have a 2000*12 matrix of expression data. I have created a distance matrix with dist() using Euclidean method. Then in hclust I have used complete linkage method. Now when I am trying to plot the dendogram with pclust method I cannot see the details of the tree. The gene names and the lower parts of the de…

updated 20.1 years ago • madhurima bhattacharjee

samples$group.1+AdiposeCPMCountGT1_min20percentsamples$samples$Gender) # To rename column names colnames(design.adipose)[1] = "MAO" colnames(design.adipose)[2] = "MHNW" colnames(design.adipose)[3] = "MHO" colnames(design.adipose...contr.matrix.Adipose = makeContrasts(MHOvsMHNW = MHO-MHNW,MAOvsMHNW = MAO-MHNW,MAOvsMHO = MAO-MHO,levels = colnames(design.adipose)[1:4]) # Voom function v = vo…

design and contrast matrix

updated 7.9 years ago • prathap1708

plotting an alignment track from sequence data that was aligned to hg19 with non-UCSC chromosome names (i.e. "1", not "chr1"). I _suspect_ the problem is to do with the chromosome names, but I am not sure. My code is as follows...chr1</span>")</code>, the error vanishes and it outputs a plot that is blank except for the plot name on the Y-axis, obviously because my b…

gviz software error

updated 7.2 years ago • laura.k.hilton

lt;- rep(names(dfs), ontCounts) row.names(ans) <- NULL ans[order(ans[["Count"]], decreasing = TRUE), ] } ## Return a list named by probes. Each element is...if (!is.null(v)) counters[[p]] <- v + 1L } } } ## return a three element list named by GO ontology ## each element is an environment keyed by top-node GO ID ## initialized to zero count. ## ## The list of …

Annotation GO probe Annotation GO probe

updated 16.1 years ago • Seth Falcon

Then, from the aggregated Sample-Celltype matrix, I made another matrix to show gene expression levels in each CellType across all samples like: ``` ###gene expression levels in each CellType across all samples gen=c(7,9,4,10,3,1

SingleCellData splatter

updated 3.6 years ago • Fatima

Error in .testForValidKeys(x, keys, keytype, fks) :   None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments. Many thanks for your help

org.hs.eg.db entrez gene identifiers genesymbols

updated 7.8 years ago • imalumberjack

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. I appreciate if any body share his/her comment

org.Dr.eg.db Entrez ID

updated 7.1 years ago • modarzi

my own nomogram using *cph* function. Next, I compute C-index through D_xy value using the function *validate* of the package *rms* . It looks like: # survival rate mod.cox <- cph(formula = Surv(time, status) ~ age + weight, data=train, x= TRUE...y= TRUE, surv = TRUE) #Get the D_xy v <- validate(mod.cox, dxy=TRUE, B=1000) v ![https://i…

survival nomogram cph 95CI

updated 5.9 years ago • huynguyen96.dnu

error ```r 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 listing of valid arguments

AnnotationHub biomaRt

updated 4.7 years ago • rohitsatyam102

data2<-rma(data) Note: http://www.bioconductor.org/data/cdfenvs/repos/ does not seem to have a valid repository, skipping Note: argument `lib' is missing: using C:/PROGRA~1/R/rw1062/library Error in update.packages2(pkgs...lib, recurse, type, force = force, : Supplied repEntry argument does not point to a valid repository. There I am .. lost ! Philippe [[alternate HTML ve…

updated 22.6 years ago • Phguardiol@aol.com

centroids of gene expression" by Tibshirani, et. al. In the paper it mentions using 10-fold cross-validation. The pamr.cv function defaults to setting nfold to the smallest class size, in this case 8. Using the khan.txt tutorial...nfold = 10 to ensure I can reproduce the results from the paper. It still only does an 8-fold cross-validation. Is this a bug or am I missing something? I'm using pamr…

Cancer pamr Cancer pamr

updated 17.8 years ago • Patricia Greninger

<div class="preformatted"> Hello, I am trying to read and work with data from an Affymetrix tiling array. (And appreciate the previous posts for working with such data)! I am using the packages "makePlatformDesign" and "oligo". I have successfully used the makePDpackage function to create the needed package (pd.at35b.mr.v04.2.tigrv5) makePDpackage("At35b_MR_v04-2 _TIGRv5.bpmap", type="…

cdf oligo cdf oligo

updated 18.1 years ago • Matt Settles

Hi all, I am having an issue with DESeq2. One is related to its use in galaxy (did not get an answer on galaxy forum so I thought why not ask here) and one is related to the introduction of coldata information in the matrix before running DESeq2 when using featureCounts data. 1) using Galaxy with 2 factors (2 batches/ 2 discinct studies from the litterature), 3 levels in each factor that ar…

DESeq2

updated 5.0 years ago • NGS_enthusiast

gt; [[6]] rs6518357 >>> >>> You need to be careful to use the same chromosome naming convention as >>> the SNPlocs package (which uses dbSNP naming convention). For example >>> in the 'mylocs' object...locs) >>> { >>> if (!is(locs, "GRanges")) >>&…

SNP Cancer SNPlocs ASSIGN SNP Cancer SNPlocs ASSIGN

updated 12.5 years ago • Fabrice Tourre

University (VCU) is seeking to fill a tenured/tenure-eligible faculty position at the level of assistant, associate, or full professor. We are seeking applicants with training and research interest in the design...of Health as well as local and regional health departments. Qualifications: For all levels, candidates should have a Ph.D. in biostatistics, statistics or relate…

Sequencing Cancer Sequencing Cancer

updated 13.2 years ago • Kellie J. Archer, Ph.D.

by ‘xcms’ But the same error is returned. Any suggestions? Here is information: ``` BiocManager::valid() * sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041...Bioconductor version '3.12' * 3 packages out-of-date * 0 packages too new create a valid installation with BiocManager::install(c( …

software error xcms MSnbase

updated 5.3 years ago • kramerl

the overall dose effect and infection effect (contrast made as above). Please go over the condition level contrasts and correct me if I'm wrong. Hope this information is not too little/confusing to understand the problem. Appreciate...Alan library(edgeR) xim <- read.delim("NreadCounts.txt", row.names=1, stringsAsFactors=FALSE) names(x) group = factor(c("WC", "WC", "WI", "WI", "LC", "LC"…

GO edgeR GO edgeR

updated 12.5 years ago • Alan Smith

<div class="preformatted">A new program in the Metrology for Gene Expression at the National Institute for Standards and Technology in Gaithersburg, MD, is under development and seeking enthusiastic and talented postdoctoral research candidates interested in exploring the basic measurement properties of microarrays. Our work will focus on understanding the performance of microarray gene exp…

Microarray PROcess GLAD attract Microarray PROcess GLAD attract

updated 21.0 years ago • Marc Salit

the AnnotationDbi package but I get an error. It says that two fields in the source DB have the same name. The same error raises when trying to get the keys for "GO" and "EVIDENCE". Could you please help me to solve this issue? Thank...to GO mapping data... Error in FUN(X[[i]], ...) : Two fields in the source DB have the same name. > sessionInfo() R version 3.6.3 (2020-02-29) Pl…

software error AnnotationForge AnnotationDbi

updated 5.6 years ago • jdiaz

scanner output); older archives like 27k COAD are structured in a format that can be extracted from level 3 (masked beta values), or else level 1 data (M and U intensities, which are fed as matrices to methylumi or minfi). Each file...data, but also some 27k data, such as LAML and KIRC) include IDAT files and a mapping from sample name to IDAT barcode, both in the MAGE-tab experiment description…

Preprocessing PROcess lumi methylumi Preprocessing PROcess lumi methylumi

updated 13.8 years ago • Tim Triche

from a affy experiment). I have 10 normals and 15 cancer lines. of 180 I have some duplicate gene names (arising from two different probesets for a single gene). I want to calculate the median expression value for these two

Clustering Cancer affy Clustering Cancer affy

updated 17.7 years ago • Srinivas Iyyer

<div class="preformatted">Hi All, For a while I have been using these lines below to normalize a large Affy data set with customCDFs and gcrma. I can't seem to make it work anymore. For some reason, in the affinity adjustment of gcrma, there is a switch to the affy CDF which gives an error later. Its a bit puzzling. I am confident the cdf name is correct and I even updated the custom CDFs …

cdf affy gcrma cdf affy gcrma

updated 14.6 years ago • Yair Benita

gave me > Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'MGI'. Please use the keys method to see a listing of valid arguments my countdata bears the ENSMUSG prefixes

org.Mm.eg.db AnnotationDbi

updated 5.6 years ago • kavator

GOCollection()) setwd("/path/") save(Sc.gsc, file = "Sc.gsc.Rda")</pre> Now, if I'm not wrong I must select the universe of genes present at my experiment. I have a list of characters with the genes that are present in my...pre> universe = Lkeys(org.Sc.sgdGO) genes = universe[1:500] params <- GSEAGOHyperGParams(name="My Custom GSEA based annot Params", + geneSetCollection=S…

gostats

updated 10.8 years ago • nonCodingGene

I have a custom annotation package which I created using "AnnBuilder" package. The package named "ipihs324" has annotation for IPI identifiers and contains mappings to Entrez ids in the environment variable ipihs324ENTREZID...Error in mget("IPI00000948", env, ifnotfound = list("FALSE")) : second argument must be an environment ########################## As I want to write a generic code for lo…

Proteomics Annotation convert Proteomics Annotation convert

updated 18.0 years ago • Chanchal Kumar

External("dotTcl", ..., PACKAGE = "tcltk"), class = "tclObj") : [tcl] ambiguous option "-col": must be -column, -columnspan, -in, -ipadx, -ipady, -padx, -pady, -row, -rowspan, or -sticky. May this have anything to do with the environment...variable set up for Tcl/Tk? I have it as follows: Variable name: TCL_LIBRARY Variable value: c:\tcl\lib\tcl8.4. Thanks again for all your suggesti…

Cancer mgu74av2 cdf probe affy Cancer mgu74av2 cdf probe affy

updated 22.6 years ago • Fátima Núñez

I have received several inquiries about a recent error in FELLA. The message, after calling **buildGraphFromKEGGREST**, looks like the following: Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : Not Found (HTTP 404) This is due to our dependency KEGGREST, so we must wait for a fix on their behalf. In the meantime, we have shared some FELLA databases f…

FELLA software error

updated 6.1 years ago • sergi.picart

Hi all, hi Michael, we want to build receiver operating characteristics for patients from two separate cohorts (using gene expression from sequencing as predictor), and I was thinking about how to compare them in this context. I did vst() (`varianceStablilizingTransformation()`) on both of them and tried to use one dataset as training set ("`pred_data`") and the other set as the test set ("`te…

deseq2 pROC ROCR glm

updated 6.5 years ago • sebastian.lobentanzer

0","0.011090163",..: 1 2 2 68 2 2 2 2 2 2 ... $ Bif : Factor w/ 52 levels "*","0","0.011137098",..: 2 1 2 2 2 2 2 2 2 2 ... $ Bill : Factor w/ 37 levels "*","0","0.010856585",..: 2 2 1 2 2 2 2 2 2 2 ... $ Blaz : Factor w/ 60 levels "*","0","0.010856585",..: 2...2 2 1 2 2 2 2 2 2 ... $ Bonn : Factor w/ 58 levels "*","0","0.010877842",..: 2 2 2 2 1 53 2 2 2 2 ... $ Bow : Factor w/ …

bioDist bioDist

updated 12.3 years ago • Guest User

values within a heatmap plot > labeledHeatmap(Matrix = moduleTraitCor, + xLabels = names(design2), + yLabels = names(MEs), + ySymbols = names(MEs), + colorLabels = FALSE, + colors = greenWhiteRed(50), + textMatrix = textMatrix, + setStdMargins...paste("Module-trait relationships…

WGCNA

updated 3.6 years ago • ayabalbaa1990

str(eset) Error in readExpressionSet(exprsFile, phenoDataFile, header = TRUE, sep = "\t") : Column names of expression matrix must be identical to the sample names of the phenodata table. You could use 'options(error=recover

updated 17.4 years ago • daphne mouzaki RI

**Dear all,** I am just a beginner of R program. I need to analyze my microarray data. So, I have just started (just 2 days only) to practice with one data set available in GEO called "GSE58231" I have compiled the script following the wiki page "Analyze your own microarray data in R/Bioconductor". However, a lot of functions don't work properly, and unfortunately, as I am a beginner, I am …

affy limma

updated 6.9 years ago • mahmudornob

Dear all, I have bed files with ChIP-seq data, with sequence (chromosome) names like this: chr1, chr10, chr11, chr12, chr13, chr13\_random, chr14, . . ., chrX I  import the bed file data into a DiffBind DBA object...Dear all, I have bed files with ChIP-seq data, with sequence (chromosome) names like this: chr1, chr10, chr11, chr12, chr13, chr13\_random, chr14, . . ., chrX I&nbs…

DiffBind ChIP-Seq

updated 11.0 years ago • Georg Otto

genes.fpkm_tracking 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)</pre> This is my session info: <pre> R version

cummerbund bug error

updated 8.4 years ago • tannerndrsn4

other). All my reading of the samtools docs suggested that there is no facility for indexing by read name as opposed to genomic coordinates, so the first way that occured to me to do this was to sort each bam by read name (which is...is really two-fold: 1) Am I right in my reading of the Rsamtools docs? Are there any lower level functions for reading bams I am ignoring that could do what I wa…

GO Rsamtools GO Rsamtools

updated 13.4 years ago • Alex Gutteridge

<div class="preformatted"> Hi, I am using limma package on HuGene2.0st array. When I tried to remove the unannotated rows (NAs) after mapping probeID to gene names. Some significant gene lists I got have the differentially expressed genes, but some of gene lists have all of the unsignificantly expressed genes. The code I used as follows: cont.matrix <- makeContrasts( inter…

probe limma probe limma

updated 12.4 years ago • Guest User

The intention is to normalise first against the abundance of these sequences (create a 'base-level abundance'), and then input the new abundances into edgeR to identify sRNA sequences that have been enriched in the samples...header =T, sep="\t") > group = sampleInfo[,2] > group [1] sample sample total total Levels: sample total > rawcounts <- read.delim("abun.tab", ro…

Sequencing edgeR Sequencing edgeR

updated 12.3 years ago • Kenlee Nakasugi

The Institute of Health Informatics in the University of Minnesota is seeking 2 masters or Ph.D. level Bioinformaticians to join a team working on multiple basic and clinical research projects in the field of sequencing...for biomarker discovery</li> </ul> <p><strong>How To Apply: </strong><br/> Applications must be submitted online. To be consider…

R bioconductor next-generation sequencing Job

updated 8.7 years ago • mmacchie

transcripts_tx_chrom, NA, "transcripts$tx_chrom", : all the values in 'transcripts$tx_chrom' must be present in 'chrominfo$chrom' In addition: Warning message: In .deduceExonRankings(exs, format = "gtf") : Infering Exon Rankings...If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName Without the "chrominfo" argument I got the…

Annotation TranscriptDb Annotation TranscriptDb

updated 12.6 years ago • Ugo Borello