Bioconductor Forum

called ctc and cluster. On the SMD website, I downloaded Xcluster for windows. In R, I write : name<-xcluster(file) R wrote : Xcluster isn't install I don't know what I must do to cluster my data. Someone can help me Thanks [[alternative

Microarray ctc Microarray ctc

updated 20.5 years ago • Antoine Lucas

<div class="preformatted">I have a simple loop of 2-color cDNA microarray experiments containing 6 individuals and 2 technical replicates for each. After batch and printtip normalization I need the intensity values for each feature, for each individual. I ran the following script using lmFit to obtain coefficients for each feature, for each individual: > design <- modelMatrix(…

Microarray Normalization Microarray Normalization

updated 17.5 years ago • Lin Huffman

VertexListGraph&, const boost::bgl_named_params<p, r="" t,="">&) [with VertexListGraph = std::vector<std::vector<long int="" int,="" std::allocator<long="" unsigned=""> >, std::allocator<std::vector<long int="" int,="" std::allocator<long="" unsigned...amp;, OutputIterator, const boost::bgl_named_params<p, r="" t,="">&) [with VertexL…

Cancer graph RBGL Cancer graph RBGL

updated 19.6 years ago • Johannes Rainer

Hi, I'm having some troubles trying to filter a SingleCellLoomExperiment object by its colData. I made a subset with 100 columns , an I want to filter by the variable Tissue in colData to be equal than "DRG". Does anyone know what I'm doing wrong? Many thanks! ``` > scle.all class: SingleCellLoomExperiment dim: 27998 100 metadata(0): assays(2): matrix logcounts rownames(…

SingleCellLoomExperiment

updated 5.7 years ago • marc.tormo

Good morning, I am working with edgeR to perform differential expression on rna-seq data. I have a design with two variables :  type (obese/normal) and treatment type is a vector with two levels (obese/normal) treatment is a vector with 5 levels ( 5 different treatments) But when I perform this line of code : design\_matrix = model.matrix(~0+type+treatment) the design\_mat…

experimental design model.matrix edger

updated 7.8 years ago • Aurora

I would like to create a PCA plot with ellipse for grouping. I have a dataset from DESeqFromHTSeqCount. I can change the color of point but could not adjust the color of ellipse. My code is below: ``` > #Set working directory for data > setwd("C:/Users/t_v026/Dropbox/Atlantic salmon/New RNAseq/DEG Analysis/RawCount") > directory <- "C:/Users/t_v026/Dropbox/Atlantic sa…

stat_ellipse DESeq2 ggplot2

updated 5.2 years ago • thu.vo

Dear Community, i would like to run in R with edgeR, some multiple conditions/contrasts, regarding different cancer subtypes, versus the control healthy tissues group of samples. The format of my Summarized experiment and my phenodata object are the following: <pre> coad_clear class: RangedSummarizedExperiment dim: 56963 497 metadata(1): data_release assays(1): HTSeq - Counts row…

edger multifactorial design multiple comparisons differential gene expression

updated 7.8 years ago • svlachavas

text as show below. ```r > seqs_aln DNAMultipleAlignment with 5 rows and 230 columns aln names [1] -----ATTGTTTAGTCTGGGGTTTACAGAAGAGTTGTTTCTTCATGGAA...TTTCGCCGAAAAATCAAG------------------GTTCCATTGAGT- Oki [2] -----ATTGTTTAGTCTGCTG...mskInd, 0)), collapse = "") + …

Biostrings

updated 3.9 years ago • Charles Plessy

div class="preformatted">Im using vennDiagram and vennCounts with 2 lists of characters (set1 and set2), to show how they compare. However I notice that vennDiagram by defaults puts an 0 outside the circles...possible, if not is there another way around it? Code: library(limma) set1 = scan("set1.txt",what='character',sep="\n") set2 = scan("set2.txt",what='character',sep="\n") set1 = set1…

updated 17.5 years ago • james perkins

nbsp;   The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list. I have used this code before multiple times including

r package problem

updated 7.6 years ago • rdpinho

pre> Obviously this interfers with annotation so have split it by + and annotated both for gene names etc. However with many of them per dataset I wondered how best to handle them quickly and easily? I know I could manually

rnaseq deseq2 ensembl

updated 8.7 years ago • Nicholas Owen

hgnc_symbol[ idx ]</pre>   I'd now like to use this on a dataframe where the input row names are transcript IDs (e.g. ENST000...). I'm not sure whether I can do this with BioMart - does anyone know

rnaseq r biomart

updated 10.1 years ago • kmuench

Reg: makePdInfoPackage Error in sqliteExecStatement(con, > >statement, bind.data) : bind.data must have non-zero dimensions > > > >Hi Nitesh, > > > > > >can you please "re-read" the ndf? use: > > > >ndf = read.table...makePdInfoPackage Error in sqliteExecStatement(con, > >…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.3 years ago • Benilton Carvalho

groking the documentation/functionality of (for instance) precede, as it seems to return an integer vector that's "backwards to" the documentation. For instance, for `precede(x, subject)`, the docs say: precede returns an integer...vector of the index of range in subject that ends before and closest to the start of each range in x. Note that any overlapping...integer vector should be the …

Cancer Cancer

updated 15.0 years ago • Steve Lianoglou

with 48 rows and 11 columns pool.plant letter tissue line pool.time time <character> <character> <factor> <factor> <character> <factor> la5.3.21 a5.3.21 C leaf a554 10-17 3 ls0.3.21 s0.3.21 F leaf s018 10-17...DESeq2/inst/doc/DESeq2.html#contrasts</numeric>…

DESeq2

updated 14 months ago • boczniak767

__Summary:__ The Center for Biomedical Informatics (CBMI) [https://cbmi.med.harvard.edu](https://cbmi.med.harvard.edu/) at Harvard Medical School is looking for a Research Associate to help build cutting edge research platforms. The real value in biomedical research lies not in the scale of any single source of data, but in the ability to integrate and interrogate multiple, complementary dataset…

reseach phenotype extraction biomedical ontologies Job

updated 11.2 years ago • Doe, Aimee

it comes down to setting the environment variable http_proxy to your proxy server (note that it must be set before starting R). If your proxy server requires a user name and password you may also have to set http_proxy_user...use the form "ftp://proxy.dom.com:3128/" where the default port is 21. These environment variables must be set before the download code is first used: they cannot be altered…

Microarray Microarray

updated 21.6 years ago • Christopher Wilkinson

to another. If you want to use different colors for the genes up and down regulated in you DE vector, you can do so by using a KEGG webpage: http://www.genome.jp/kegg/tool/map_pathway2.html The code below generates a text...genes in blue and the unregulated ones in red. I hope this helps, Adi org="hsa" DE=c(-1,-1,1,1); names(DE)<-c("1622", "116519", "4199","7350") up<-names(DE[D…

Pathways Organism SPIA Pathways Organism SPIA

updated 14.1 years ago • Tarca, Adi

<div class="preformatted"> Dear Valerie, thanks a lot for making your great ensemblVEP package available. I have been using it to assess the consequences of variants detected by the VariantTools package (version 1.6.1). ensemblVEP retrieves the variantEffectPredictor output, but triggers a number of warnings (see below). library(ensemblVEP) ## example.vcf is available at http://dl.dropb…

Coverage VariantTools ensemblVEP Coverage VariantTools ensemblVEP

updated 12.7 years ago • Guest User

bin/windows/contrib/3.1 Error in install.packages : STRING_ELT() can only be applied to a 'character vector', not a 'NULL' 'biocLite.R' failed to install 'BiocInstaller', use 'install.packages("BiocInstaller", repos="https...bin/windows/contrib/3.1 Error in install.packages : STRING_ELT() can only be applied to a 'character vector', not a 'NULL' sessionInfo() R version 3.1.0 (2014-04-10…

ToPASeq Deprecation

updated 3.7 years ago • pgauthi1

to make sure I understand coding of phenotypic label in poe.mcmc function of metaArray correctly. Vector of my arrays' treatments could be presented as: (ctrl, ctrl, ctrl, trt1, trt1, trt1) so as NN value I used vector (1, 1, 1, 0, 0, 0). Documentation...Although this three documentation files suggests the same coding, fit.em states that: " cl: A vector of 0s and 1s. Use 1 for normal phenotype…

metaArray metaArray

updated 14.3 years ago • Maciej Jończyk

for my analysis. I have two files for the data: one is an Excel file (including time points and the names of the samples, such as "stimulated vs. non-stimulated" controls), and a text file containing gene expression data (RNA-seq...library (DESeq2) coldata <- data.frame(row.names = colnames(GeneMat), condition) #check if col names = row names ## must say TRUE all(rownames(coldata) == c…

DESeq2 ctsGE

updated 21 months ago • Emma

<div class="preformatted">Dear all, I am analyzing data obtained using the HuGene2.0-st arrays from affymetrix. I have used aroma for preprocessing and limma for diff. expression analysis. After multiple testing I lost significance and therefore I want to filter out genes that do not have a potential to be significantly different. So I have created an expression set after rma plm &l…

Annotation Preprocessing hgu95av2 limma Annotation Preprocessing hgu95av2 limma

updated 12.8 years ago • Andreia Fonseca

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 2.3 years ago • Rockbar

will give me 3605 for the HDAC1_HUMAN protein. I am trying to do exactly this in RStudio with a vector of UniProt IDs that I want to convert to Entrez IDs. However, I couldn't manage and therefore wanted to ask whether someone...but cannot get a hold of which function to use. So what I want to achieve is the following: Input vector: ```c(HDAC1_HUMAN,RIR2_HUMAN,PK3CG_HUMAN,TOP1_HUMAN,TOP2A_HUMA…

ID Uniprot EntrezID

updated 3.6 years ago • tom.kloter

is.character(type)) { i = match(type, CURLcodeValues) typeName = if (is.na(i)) character() else names(CURLcodeValues)[i] } typeName = gsub("^CURLE_", "", typeName) fun = (if (asError) stop else warning) fun(structure(list

updated 13.5 years ago • Guest User

from GOstats. I get the following error: Error in initialize(value, ...) :    invalid names for slots of class “GOHyperGResult”: pvalues, oddsRatios, expectedCounts, catToGeneId, organism Here the code I use: <pre

gostats

updated 8.1 years ago • laianavarromartin

keep getting an error message saying: <pre> (data, reference, dnn = dnn, ...) : all arguments must have the same length</pre> I assume this must be in relation to my list of markers, but am unsure why this is occurring. I have...is the marker list.  <pre> w <- table(fData(msnsetmarkers)[, "markers"]) w <- 1/w[names(w) != "unknown"] # the part I g…

bioconductor proloc

updated 7.8 years ago • sjp221

An object of class â"kmeans"â which is a list with components: >> >> cluster: A vector of integers indicating the cluster to which each >> point is allocated. >> >> If you have problems, please read

Clustering probe Clustering probe

updated 15.6 years ago • Sean Davis

p, r="" t,="">&, boost::detail::error_property_not_found) [with VertexListGraph = std::vector<std::vector<unsigned int="">, std::allocator<std::vector<unsigned int=""> > >; Vertex = unsigned int; DFSVisitor = boost::topo_sort_visitor...VertexListGraph&, const boost::bgl_named_params<p, r="" t,="">&) [with VertexListGraph = std::vect…

graph RBGL PROcess graph RBGL PROcess

updated 13.7 years ago • Guest User

I have a vector GO IDs (`` go.vec ``) for which I'd like to measure the shortest-path distance in the `` GO `` `` DAG `` `` graphNEL ``. The only way I can think...I have a vector GO IDs (`` go.vec ``) for which I'd like to measure the shortest-path distance in the `` GO `` `` DAG `` `` graphNEL ``. The only way I can think of...nbsp; dists <- dag.sp(go.dag,start=go.dist.df$go1[n])[[1]]&…

graph rgbl dag

updated 9.1 years ago • rubi

<div class="preformatted">I am using the writeVcf() function in the VariantAnnotation package, which I understand to be 'under construction' from the documentation. I am wondering why writeVcf() is taking so long to do it's job and if there is anything I can do to speed this up? For example, I have a VCF object containing some 36,000 variants that I want to write to file and this takes near…

VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation

updated 13.2 years ago • Peter Hickey

1)) > ikGvcf <- readVcf(ikGFile, 'hg19', param = param ) > rowRanges(ikGvcf[duplicated(names(ikGvcf))]) GRanges object with 3 ranges and 5 metadata columns: seqnames ranges strand | paramRangeID REF <rle> <iranges> <rle...ALT QUAL FILTER <char…

software error

updated 6.4 years ago • sskimb

X11. ===================== If an R package is going to use Tcl/Tk then the interface package tcltk must be installed into R. (It is installed with a standard install of R). If an R package uses Tcl/Tk then Tcl/Tk must be installed...if at all), are installed on unix based computers( including Mac OSX), use the command: %find / -name "BWi*" -print 2>/dev/null (Use man on the find command…

limmaGUI affylmGUI

updated 16 months ago • Keith Satterley

did not work as expected.  <s>Somehow the margin was defined by the maximum of the specified vector, so I am wondering wether this behaviour is intended or a bug. </s>   Anyways, thank you for providing the awesome...genome="hg19", feature="test", group=gr, id=paste("annTrack item", 1:4), …

gviz grid layout

updated 7.1 years ago • alex.gos90

do.logtransform = TRUE) The directory 'MLL' has been created. Error : cannot allocate vector of size 77.4 Mb KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 (loaded the KernSmooth namespace) [[1]] [[2]] [[3]] Error in aqm.report.qm...p, obj[[i]], i, names(obj)[i]) : could not find function "svg" In addition: Warning message: In arrayQualityMetrics(expressionset = MLL.A, outdir...not d…

updated 15.1 years ago • Lavinia Gordon

<div class="preformatted">Hi, I look at the slot genes in fit2 (fit2$genes) and selected.dif. Both have the some number of genes. But, when I try fit2$genes[selected.dif,] I get a error message: Error in "[.default"(fit2$genes, , selected.dif) : incorrect number of dimensions If I use topTable and set the coef slot to 1, 2 or 3 I get the DE genes, but, I suppose that in these …

Annotation limma Annotation limma

updated 20.9 years ago • Marcelo Luiz de Laia

an error that the header files cannot be found. After consulting the read_me, I concluded that it must be that ChemmineOB cannot find the open babel files. So I set out to specify the correct paths using: `R CMD INSTALL --configure...cannot be found. Unfortunately this babelconfig.h file is in a different (although closely named) directory: openbabel-openbabel-2-4-0/build/include/. (notice i…

ChemmineOB Linux Installation

updated 6.8 years ago • jandrosavich

<div class="preformatted">Hi Mousami, Yes, you can use data matrix or vector for sure. With pathview package loaded, just check the help info for the pathview function by typing in: ?pathview Read the description for argument ?gene.data?. The .rda is just a data file format for storage in the hard disk, after loading the data into R (console or command line session), you get your R data ob…

pathview pathview

updated 12.5 years ago • Luo Weijun

<div class="preformatted">Hi all, I'm struggling with the meta-analysis of microarray data. In the user guide of the bioconductor package "MAMA" there is an exemple of meta- analysis in cancer microarray data concerning the comparison of expression profiles in MSI (microsatelite instable) and MSS (microsatelite stable) colon cancer. Data are gathered from three microarray experiments from …

Microarray Cancer Colon limma Microarray Cancer Colon limma

updated 14.4 years ago • Manuela Di Russo

LP", chip = "org.Hs.eg.db") Error in .get_eg_to_go_fun(mapfun, chip) : either mapfun or chip must be specified In addition: Warning message: object 'org.Hs.egGO2PROBE' not found DB-based version of org.Hs.eg.db not...LP", chip = "hgu133plus2.db") NA</pre> The argument description says: <pre> chip The name of a DB-based annotation data package (the name will end in …

gostats

updated 9.4 years ago • Lluís Revilla Sancho

and getting a clean data frame with counts (I'm using limma voom for differential expression), and a named vector with gene lengths. 2. I am then running the following code (as a first step before testing GO enrichment of genes...in contrast 1 of interest): <pre> goBiasLength <- counttableCompleteLen.vector[order(match(names(counttableCompleteLen.vector),names(results[,"Contrast1"…

goseq

updated 9.5 years ago • Darya Vanichkina

step, checkFunc = function(...) TRUE){ n <- length(obj) if(width < 1){stop("Window width must be ≥ 1.")} if(step < 1){stop("step must be ≥ 1.")} if(any(width > n)){stop("The window size cannot be greater than number of data elements.")} state...lt;- new.env() state$i <- 0L state$obj <- obj if(is.null(ref)){ state$ref &…

dnastringset parallel iterators

updated 10.1 years ago • ben.ward

Users/user1/Desktop/Plant_1/eqtl/Gene_expression.txt.", sep = "") #covariates_file_name to character() Error: unexpected symbol in "covariates_file_name to" covariates_file_name = character() output_file_name = tempfile

MatrixEQTL

updated 3.9 years ago • Neha

with certain input tables that should work... the problem was in the quotes ("): files containing (") characters delimiting textual cells did not work. Now the problem is solved and you can upload tables containing (") characters

updated 18.1 years ago • Juan C Oliveros Collazos

not only to supply Sample_platform_id, but also a "Sample_platform_title" which would contain the name of the chip as given by the manufacturer. 3, Sample descriptions: Since most data are useless w/o the sample description...GSExxxx # gse: GEOqueryclass imported from GEO GSE file GSExxxx_family.soft (or soft.gz) # column: name of column to be extracted from data table # load libraries l…

hgu95a hgu95av2 GEOquery hgu95a hgu95av2 GEOquery

updated 20.0 years ago • Christian.Stratowa@vie.boehringer-ingel…

can give me some insights and suggestions?    Below is chunk of my data: >`` dxr[name,] `` `` LRT p-value: full vs reduced ``   `` DataFrame with 3 rows and 13 columns `` ``                  groupID...nbsp;       stat `` ``    &am…

dexseq

updated 9.8 years ago • Chao-Jen Wong

_mart\_91" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL\_MART\_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />   <MartURLLocation..._mart\_91" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL\_MART\_ONTOLOGY" path="/bio…

TCGAbioloinks GDC data

updated 7.8 years ago • lawarde.ankita1

giving the analysis more power to detect differential expression. ``` # genes object is a character vector containing the names of genes-of-interest genes[1:5] ## "PPP3CB_AS1" "IL10RB_AS1" "PPP1R26_AS1" "RRN3P2" "AC099343.3...LINC01778" "AL353622.1" colnames(de_df)[1:5] ## [1] "V1" "V2" "V3" "V4" "V5" # Reassign column names. There will be duplicate column names because of biol…

R limma TPM rnaseq differential expression

updated 6.3 years ago • atakanekiz

FALSE, labels = files$Summary, group = files$group) ``` where 'files' is a spreadsheet of file names, and 'group' is a unique indicator for each possible combination of origin, regime, and assay temp (36 groups). I tried using...numeric and character string names for each group, for what it's worth. I did it at this stage because the filterByExpr() function works best

edgeR

updated 2.3 years ago • alex.hart

gt; allgenes<-as.matrix(read.table("H:\\test\\allgenes.txt", row.names=NULL, header=T, colClasses='character'))[,1] Many thanks John -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: allgenes.txt URL: <https...next part -------------- An embedded and charset-unspecified text was scrubbed... Name: siggenes.txt URL: <https: 1a59d27…

Pathways Breast siggenes PROcess cycle graphite Pathways Breast siggenes PROcess cycle

updated 12.9 years ago • array chip

div class="preformatted"> getAllQCProbes("ygs98cdf") produces the following vector of yeast control probes on the YG_S98 Affymetrix microarray chip: [1] "AFFX-YFL039C3_at" "AFFX-YFL039CM_at" "AFFX-YFL039C5_at...YER022w5_at" "AFFX-YER148w3_at" "AFFX- YER148wM_a" [9] "AFFX-YER148w5_at" The 8th component of this vector is missing a 't' at the end. When I use simpleaffy with gc.affy(AffyBatch) I…

Microarray simpleaffy Microarray simpleaffy

updated 21.1 years ago • Straubhaar, Juerg

<div class="preformatted">Hi Michael, On 7/8/2011 1:36 PM, Michael Bauer wrote: > I'm one of the system administrators at Heather's site. I have a message > to the list languishing in the moderation queue, which asks the simple > question: given R, Bioconductor, the data set, and that error message, > how do I extract what additional package(s) it needs to insta…

Microarray Annotation cdf probe cycle Microarray Annotation cdf probe cycle

updated 14.5 years ago • James W. MacDonald

online and when I download database) and in hgu133plus2.db, I can't see them associated with gene names.   For instance, I can use two methods to get gene names: <pre> biocLite(hgu133plus2.db) biocLite(annotate) r=rownames

Annotation hgu133plus2

updated 8.9 years ago • benoit.tessoulin

ensembl_transcript_id 1 ENST00000232424 Error in rec$desc : $ operator is invalid for atomic vectors > gene.string $desc [1] ">HES1|ENSG00000114315|ENST00000232424" $seq [1] "GGGGGCTCAGGCCACCCCTCCTCCTAAACTCCCCAACCCACCTCTCTTCCCTCCGGACTCTAAAC...AAAAT" > writeFASTA (gene.string, zz) Error in rec$desc : $ operator is invalid for atomic vectors > -----Messaggio ori…

Biophysics Biophysics

updated 16.5 years ago • mauede@alice.it

<div class="preformatted">Hi- The minOverlap parameter in dba.read provides a simple way to define a consensus peakset used for further analysis. In cases where you have loaded a number of different peaksets, a single consensus peakset is defined consisting of (merged) peaks that overlap with at least X of the original peaksets. So if X=1, then all the (merged) peaks are included in the co…

DiffBind DiffBind

updated 11.9 years ago • Rory Stark

calculate something ... } # Error in .normarg_nzdata(nzdata, nrow(nzindex)) : # 'nzdata' must be a vector sessionInfo( ) # R version 4.1.0 (2021-05-18) # Platform: x86_64-pc-linux-gnu (64-bit) # Running under: Ubuntu 20.04.2 LTS

DelayedArray

updated 4.6 years ago • Koki

for(i) [1] "1 of 3" Error in matrix(unlist(GTstr), ncol = 2, byrow = TRUE) :    'data' must be of a vector type, was 'NULL' > write.csv(results, file = "missense_snps.csv", quote = F, row.names = F) > traceback() 3: matrix(unlist

bioconductor vcf

updated 8.8 years ago • bkauf

perm") This function calls mt.minP with classlabel=Y. From the documentation: classlabel: A vector of integers corresponding to observation (column) class labels. For k classes, the labels must be integers between 0

updated 20.6 years ago • kpollard

logCPM=(glmfit$abundance+log(1e6))/log(2), [....] logFC is matrix, inheriting its column name from the matrix product at ** (if only one contrast was passed, will be the name of the contrast). Then, when building the value...data frame at ***, the name given in the LHS of the assignment is ignored (because logFC is a matrix). The resulting tab has no logFC column. One possible...fix would be to…

Cancer edgeR Cancer edgeR

updated 13.1 years ago • h.soueidan@nki.nl