Bioconductor Forum

fails", this is what happens: (a) if I add --internet2 to the target of the shortcut: [The name '"C:\Program Files\R\R-2.2.1\bin\Rgui.exe"--internet2' specified in the Target box is not valid. Make sure the path and file name

updated 19.8 years ago • Amy Mikhail

I am trying to use the topGO package but I get this error message "Error in .local(.Object, ...) : allGenes must be a named vector" when I execute the following command. ``` # Data preparation of reference dataset selGenes <- genefilter(fitted, filterfun(pOverA(0.20, log2(100)), function(x) (IQR(x) > 0.25))) eSet <- fitted[selGenes, ] AllNames <- rownames(eSet) head(A…

Ensembl ensembldb

updated 5.0 years ago • H. Stotz

which="userinfo:fIntenQuant", range=1.5) ### images of raw data (no longer necessary to attachInten()) names <- unlist(treeNames(data.gene)) image(data.gene, names=names[4], add.legend=TRUE) ### save image as png-file outfile <- paste...Image_", names[4], sep="") plotImage(data.gene, type="intensity", names=names[4], dev="png", outfile=outfile) ### density plot outfile <- …

xps xps

updated 14.6 years ago • cstrato

in edgeR): <pre> Ind <- factor(exp.design$ind) Phenotype <- factor(exp.design$phenotype, levels = c('Phen1', 'Phen2')) Treatment <- factor(exp.design$treatment, levels = c('Comp1', 'Comp2')) Group <- factor(paste(exp.design$phenotype...exp.design$treatment, '.', levels = c('Phen1.Comp1', 'Phen1.Comp2', 'Phen2.Comp1', 'Phen2.Co…

deseq2 multiple factor design

updated 8.5 years ago • Vladimir Krasikov

I am confused whether I am doing correctly or not. ``` > contrastm <- makeContrasts(mm, levels = design1) Warning message: In makeContrasts(mm, levels = design1) : Renaming (Intercept) to Intercept >contrastm Contrasts...Levels mm Intercept 0 mm 1 > fit2 <- contrasts.fit(fit, contrastm) Warning message: In contrasts.fit(…

limma

updated 6.0 years ago • sujata

when using txOut = FALSE (default) because I want the values from StringTie quantification but gene level summarized (as they are more robust). I am using "StringTie" output files "t_data.ctab" as input files for tximport. tximport...gives the lists with matrices, “abundance”, “counts”, and “length” where the transcript level information is summarized to the gene-level. I want to ask whether …

tximport

updated 6.8 years ago • HKS

function(id) { return(paste("tophat-juncs-", id, sep="")) } ) groups <- as.factor(sapply(names(files), function(filename) { ifelse(grepl(filename, tameFileNames), "tame", "aggr") })) # Initial data analysis over all chromosomes...addition: Warning message: In .Seqinfo.mergexy(x, y) : The 2 combined objects have no sequence levels in common. (Use suppressWarnings() to suppress th…

derfinder

updated 11.1 years ago • jessica.hekman

L17328" "S81916" "U63332" "M77235" and I would like to find ( in a repository for ex.) the names as: [1] "hypothetical protein LOC221823" [2] "meningioma (disrupted in balanced translocation) 1" [3] "fasciculation and elongation

proteinProfiles ProteomicsWorkflow ProteomicsAnnotationHubData Proteomics

updated 4.3 years ago • ALOK

<div class="preformatted">Hi, We are recruiting for bioinformatics positions (post-doc, junior, senior faculty) at Georgetown University's Innovation Center for Biomedical Informatics (ICBI). The center website is: http://icbi.georgetown.edu/ The position description (for a faculty level) is attached. We are also recruiting for more junior level positions with similar skills, experience …

updated 13.1 years ago • Subha Madhavan

I have rnaseq data for various combinations of three different factors (let's call them X, Y, and Z).  Some of these combinations represent controls, and the rest represent treatments. I want to perform differential gene expression analysis for various pairs of treatment and control combinations. I can't figure out how to specify the `` design `` parameter for this sort of analysis. I…

deseq2

updated 9.2 years ago • kjo

sometimes, even with very high adj.P.Val, with decent P.Value (e.g., <0.01), we can have good validation. In this case, now we validated two miRNAs from the list both with good P.Value <0.01 but with rather high adj.P.Val...both are around 0.97 or 1). We did validate one of them as good miRNA but the other one is bad (we can not validate it as differential). I understood it is more…

miRNA limma miRNA limma

updated 14.5 years ago • Yi, Ming NIH/NCI [C]

So far I have performed all my analyses on UNFILTERED Illumina data from Genome Studio. Is it still VALID for Illumina data to use unfiltered data in contrast to filtered probes (comparing to background signal) with a particular...gt; I am assuming when performing hierachical clustering on the full data, the genes at background level will not significantly contribute to the clustering. However, I…

Microarray Annotation Normalization Clustering probe limma Microarray Annotation probe

updated 12.4 years ago • Wei Shi

fout <- data.frame(fout) return(fout) } ``` If I want to perform the single base-level F-statistics, instead of using the: ```r models <- makeModels(sampleDepths, testvars = pheno$group, adjustvars = pheno[, c("gender

derfinder

updated 4.4 years ago • Konstantinos Yeles

However, from the sparse doc, it is not easy to see how I can just add information like : final level nodes names & maybe propose a color rectangle. Thanks in advance

tbl_graph ggtree dendogram tree

updated 2.7 years ago • christian.dina

have two questions how to further proceed. 1) How can I get a table with all the gene expression levels? 2) How can I compare the Row labeling to the gene information from the CHIP that was used for the Assay? I know that there...is a package for the CHIP infos that I need but I have no idea how to assign the gene names to the IDs. I am not very familiar with R, so please excuse that …

GEO expression GEOquery

updated 5.6 years ago • lsbew

vr\_new, BSgenome.Hsapiens.1000genomes.hs37d5) Error in .getOneSeqFromBSgenomeMultipleSequences(x, name, start, NA, width,  :   sequence chr1 not found In addition: Warning message: In .Seqinfo.mergexy(x, y) :   The 2 combined...objects have no sequence levels in common. (Use   suppressWarnings() to suppress this warning

somaticsignatures

updated 9.4 years ago • poojitha.ojamies

and (2) whether we need the matched timepoint controls. part (1) sounds like a leave-one-out cross validation problem, but i'd appreciate anyone else's advice here. I've come across the MCREstimate package on BioC, and was wondering...time 0 control. It already looks like the timepoint controls are very similar to the t0, but there must be a more elegant way to quantify this. Here's where I sta…

updated 16.2 years ago • Mark Cowley

WT and MUT. Another question is if the healthy hemispheres differ significantly in gene expression levels (mut vs. wt). > head(metaData) ID genotype hemi 1 WT_1 WT Contra 2 WT_2 WT Contra 3 WT_3 WT Contra 4 WT_1 WT Ipsi 5 WT_2 WT Ipsi...variables or interaction terms in the design formula are linear combinations…

DESeq2 paired

updated 4.3 years ago • annamariabugaj

170 89 37 14 2 1 ------------------------------------------------------ Replication at Probe level- MEDIAN CV Error in apply(ddDUP$G[index, ], 2, sd) : dim(X) must have a positive length Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman

Cancer probe Cancer probe

updated 15.5 years ago • Richard Friedman

you to have some information about genefilter package. I am a biologist and a pre-doc student, I must admit that I am quite new to microarray data analysis and R. I'm analyzing Agilent single color gene expression data and...like the "Present" call). I particular, I want to filter out the genes that have a lower expression level than the background. I read that genefilter package has several met…

Microarray genefilter limma Microarray genefilter limma

updated 12.1 years ago • Hervé Pagès

first data(twoGroups) #when I instantiate a DataTrack object: dTrack<- DataTrack(twoGroups,name="Uniform") #I got this error:Error in DataTrack(twoGroups, name = "Uniform") : #A chromosome must be specified for this annotation...track. #so I add a chromosome, which works fine... dTrack<- DataTrack(twoGroups,chromosome="chrX",name="Uniform") #the next error occurs when I try to plot …

Annotation Annotation

updated 13.4 years ago • Guest User

unlistData = new("GRanges", seqnames = new("Rle", values = structure(integer(0), levels = character(0), class = "factor"), lengths = integer(0), elementMetadata = NULL, metadata = list()), ranges = new("IRanges", start = integer...0), width = integer(0), NAMES = NULL, elementType = "ANY", elementMetadata = NULL, metadata = list()), strand = new("Rle", val…

DESeq2 DifferentialExpression

updated 17 months ago • nhaus

logi FALSE > .. .. .. ..$ dim :List of 2 > .. .. .. .. ..$ sample:List of 8 > .. .. .. .. .. ..$ name : chr "sample" > .. .. .. .. .. ..$ len : int 1 > .. .. .. .. .. ..$ unlim : logi TRUE > .. .. .. .. .. ..$ id : int 1 > .. .. .. .. .. ..$ dimvarid : num 1 > .. .. .. .. …

SNP Annotation cdf GWASTools SNP Annotation cdf GWASTools

updated 12.5 years ago • Stephanie M. Gogarten

Downloading: 240 B Downloading: 240 B Error: failed to load 'AnnotationHub' resource name: AH49186 title: Homo_sapiens.GRCh38.dna.toplevel.fa reason: 2 resources failed to download In addition: There were...warnings: <pre> 31: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 32: In curl::curl_fetch_disk(url, x$path, h…

AnnotationHub

updated 10.1 years ago • Johannes Rainer

list",length(levels(bb$rname))); # startlistrev = vector("list",length(levels(bb$rname))); # names(startlistfwd) = levels(bb$rname); # names(startlistrev...levels(bb$rname); # startlistfwd[] = list(list()) # startlistrev[] = list(list()) # } # startlistfwd, startlistrev # # ### Keep only primary reads # { # keep...offset = length(star…

log timer

updated 2.8 years ago • Anushka

div class="preformatted">Hi User, I am trying to plot my M-A levels using different colors for the controls. For that I created a spottype file, which looks like that: SpotType ControlType...Color gene 0 black NC -1 green PC 1 red In my agilent files I don't have columns named "ID" or "Name", But I can sperate my controls with the ControlType column. This I also read in …

Annotation Annotation

updated 13.4 years ago • Assa Yeroslaviz

<div class="preformatted">Hello, I was just trying to update Bioconductor (I'm running R1.8.0) under w2k via the reposTools. However, I did not succeed. Here's the messages: > install.packages2(method="wget") Note: argument `lib' is missing: using C:/PROGRA~1/R/rw1080/library Note: http://www.bioconductor.org/CRANrepository does not seem to have a valid repository, skipping Note: h…

reposTools reposTools

updated 22.2 years ago • Arne.Muller@aventis.com

No matter what I do, I get the following error message: when the supplied 'genome' vector is named, the names must match the seqnames As far as I can make sense of this message, it seems that there is some mismatch between...found some interesting mismatches: The genome in the VCF file is denoted as "b37" and the sequence names are not 100% compatible with hg19. The lengths of chromosomes 1…

VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation

updated 12.6 years ago • UBodenhofer

nbsp; 'clear\_cluster' receive data failed:   reached elapsed time limit Error in names(res) <- nms :    'names' attribute \[143\] must be the same length as the vector \[48\] I am not sure what the names(res) refers

dexseq genomicalignments genomicfeatures genomicranges

updated 7.1 years ago • A

How to convert multiple protein fasta sequences into their gene/protein name

GenePrediction

updated 3.1 years ago • AROCKIYA

Hello, I'm working with transcript IDs as the species I'm working with is a non-model, so now that I managed to produce Volcanoplots from the contrasts: Example: ``` cont.matrix1 <- makeContrasts(ConeVsRoot=Cone-Root, levels=design) fit.cont <- contrasts.fit(fit, cont.matrix1) fit.cont <- eBayes(cont.matrix1) summa.fit <- decideTests(cont.matrix1...from the contras…

limma edgeR Glimma

updated 2.9 years ago • Mohammad

I'm using TopGo to do GO analyses. When I get my enriched terms, the long term names get corrupted. ```I have some text then ...```. For example: ``` GO:0000122 negative regulation of transcription by ... GO:0006886 intracellular...candidate_list_1[keep1] geneList1 <- factor(as.integer(bg_genes %in% candidate_list_final1)) names(geneList1) <- bg_genes GOdata1 <- n…

go software error topgo rna-seq

updated 5.5 years ago • morteza.aslanzadeh

with me. FIRSTLY SOME WORDS ABOUT OUR SAMPLES: We did experiments with two groups of test animals namely treated "T" and control "C" (without treatment) groups. Bot T and C have 20 subjects each. We took samples 4 times with 2-week...the answers for our research questions based on the current data by using edgeR? And how, in high-level view? 2. I am thinking since we have the pools (biological …

Sequencing edgeR MEDIPS Sequencing edgeR MEDIPS

updated 11.3 years ago • Vang Le

Hi, I am running some RNASeq analysis with two experimental factors, namely time (two-level factor) and genotype (three-level factor). In cases like this, I like using edgeR cause, among other reasons...Hi, I am running some RNASeq analysis with two experimental factors, namely time (two-level factor) and genotype (three-level factor). In cases like this, I like using edgeR cause, among other r…

rnaseq edger statistics model matrix

updated 8.2 years ago • David Rengel

Hello everyone,I have been struggling to the problem about how to read in bead-level txt file provided by GEO using beadarray::readIllumina, but I have no more idea to solve this. The documents by beadarray...didn't show an example for bead-level txt but other formats such as .bab and .tiff in 'BeadArrayUseCases'. My data from GEO raw data is as follows: <pre> #file: GSM1105686_88392650…

beadarray bead-level GEO lumi

updated 9.7 years ago • gnilihzeux

__moduleEigengenes()__.  I used __cbind() __\[or__ merge()__ \] function to combine the gene names and the module/color symbols. Although in this case the order of the rows is always the same, this seems not safe to me. The...dynamicMods) <span style="background-color:Yellow">genesMatchcolors <- cbind(dynamicColors, names(datExpr))</span> write.csv(genesMatchcol…

WGCNA cbind merge match gene names and Eigengene/module/colorlabels

updated 8.0 years ago • yifangt

go_cellular_component__dm_name_1006 Please use the function 'listAttributes' to get valid attribute names and if you list the attributes... listAttributes(ensembl) you can see they're indeed not listed... am I right

GO biomaRt GO biomaRt

updated 14.6 years ago • J.delasHeras@ed.ac.uk

library('DESeq2') countMatrix = read.table("RPR_count.txt",header=T,sep='\t',check.names=F) dim(countMatrix) > head (countMatrix) HRPR_0D_V8_R1 LRPR_0D_V8_R1 HRPR_0D_V8_R2 LRPR_0D_V8_R2 1 ENSRNA049455608 27 15 13 20 2 ENSRNA049455955 50 31 66 20 …

deseq2

updated 6.6 years ago • nabiyogesh

<div class="preformatted"> Hi Dr.Carvalho, > ndf = read.table("100929_HG19_Deluxe_Prom_Meth_HX1.ndf", >stringsAsFactors=FALSE, sep='\t', header = TRUE) > head(ndf) PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA 1 537151_1_25 BLOCK1 interval rank target_tm:76.00;probe_tm:77.60;freq: 9.25;count:01;rules:0000;score:0812 2 537…

Annotation PROcess pdInfoBuilder charm Annotation PROcess pdInfoBuilder charm

updated 12.3 years ago • Nitesh Turaga

**Cures Start Here.** At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transplantation led to the development of immunotherapy, which harnesses the power of the im…

job seattle Job

updated 6.5 years ago • Fred Hutch (Recruiting)

[**Please visit our careers page for more information and to apply online**][5] **Cures Start Here.** At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow transpl…

genomics seattle bioinformatics data science statistics Job

updated 5.5 years ago • Fred Hutch (Recruiting)

which appear green, red and yellow in the plot nAttrs$label <- nodesNames nAttrs$height <-"3" names(nAttrs$height) <- "height" nAttrs$fontsize <- "20" names(nAttrs$fontsize) <- "fontsize" plot(mapkG, "dot", nodeAttrs=nAttrs) I tried...message ('Error in buildNodeList(graph, nodeAttrs, subGList, attrs$node) : the character vector must have names") came up. I …

KEGGgraph KEGGgraph

updated 15.0 years ago • Unger, Kristian

I am currently working on a single-cell data analysis project, and I am facing a challenge regarding the aggregation of single-cell data into pseudobulks for input into the GSVA software. GSVA only accepts a gene X subject matrix, which means that pseudobulks must be created to facilitate this input. I have come across two different approaches to the aggregation process and I am unsure of which o…

pseudobulk scRNAseq GSVA

updated 2.6 years ago • Tadeoye

WIMM. Applicants should have a track record in mathematics or statistics ideally at the MSc or PhD level. Further details regarding the CBRG are available at http://www.cbrg.ox.ac.uk/. For further details about the position...To apply please send a CV and covering letter giving details of three referees, one of whom must be the current or most recent employer to Carol Eaton, Weatherall Institu…

updated 15.8 years ago • Steve Taylor

DOSE <span style="line-height:1.6">> require(DOSE)</span> > data(geneList) > gene <- names(geneList)\[abs(geneList) > 2\] > <span style="line-height:1.6">ggo <- groupGO(gene = gene, organism = "human", ont = "BP",level = 3, readable...TRUE)</span> __Error in groupGO(gene = gene, organism = "human", ont = "BP", …

error

updated 9.2 years ago • zhaoxiao

applied to a flowSet. I realize that to split without using the 'population' argument all samples must have the same populations, which is not the case here. Plotting the result of the filter shows populations 'area 1' through...gt; nk <- split(Data(wf[['NK-']])[c(1,2,5)], filter_cv2_cd3, population="area 3") Error in `names<-`(`*tmp*`, value = c("rest", "area 1", "area 2", "area 3"…

updated 14.7 years ago • Aric Gregson

the output to be A B [1,] 2.5 10 [2,] 3.5 11 [3,] 4.5 12 I can do this by looping through each level of the column name, but I was wondering if there is a function for calculating the average of replicates in one step. Thank

updated 14.7 years ago • Wendy Qiao

I've some lists as many as those annotated by it and these lists are indexed by the Genes Symbols/Names and then there are the statistical estimates and the Methylation level. I was able to get as many lists but this time indexed...of this type by dmpFinder in the Minfi package version 1.8.9) as many lists indexed by Genes Symbols/Names associated with these positions/sites. I'd appreciate any …

minfi minfi

updated 11.6 years ago • Giovanni Calice

can i access vector of a column in phenotype data frame if  i don't know the conditions(groups) name in the phenotype data frame . I have phenotype information in the below file Files               &nbsp...file.txt",sep="") unique <- unique(pdata$Groups) f <- factor(pdata$Groups, levels=unique) desig…

r limma

updated 10.5 years ago • hashmi

<div class="preformatted">Dear Jorge, Please see the vignette "APTvsXPS.pdf" for a comparison between APT and xps, and see Figure 25 for the reason why xps did not implement PLIER. I do not think that you can import the APT output into xps, at least not from within R (although it might be possible from C++, but I would have to check). Best regards Christian On 6/2/12 5:20 PM, Jorge Mir?…

cdf affy plier xps cdf affy plier xps

updated 13.5 years ago • cstrato

Hi, all,       I aligned my RNAseq raw data to cDNA using Kallisto and import the result using _tximport_ as suggested by the DESeq2 tutorial (tx2gene maps ensembl\_transcript\_id to ext\_gene symbol) <pre> txi.kallisto_gene <- tximport(files, type = "kallisto", tx2gene=tx2gene,ignoreTxVersion=TRUE)</pre> When I looked into the &…

deseq2

updated 4.8 years ago • Raymond

scater's runPCA/calculatePCA are unable to run parallel using MulticoreParam() This error also leaves whatever cores have been started running and does not terminate them when the code errors out. Is there a workaround of fix for this? Thanks, Dave # # BEGIN REPREX # # ```r > suppressPackageStartupMessages({ + library(TENxPBMCData) + library(scater) + lib…

calculatePCA BPPARAM scater BiocParallel runPCA

updated 4.5 years ago • doliv071

Dear all, please could you advise : how does MAFTOOLS treat the annovar files with the gene names ? For examples, shall I have a file (below), the questions would be : <span style="background-color:Yellow">> head(var.annovar.maf

maftools

updated 8.8 years ago • Bogdan

month, the offer of the company that has been co-operating with us for last 14 years. The offer is valid on all the territory of Australia, New Zealand, United Kingdom, Europe. As a leader in the career building, we recommend...account from clients of the company. After procedures of transaction dcouments preparation he/she must transfer the sum to accounts advised by our dispatchers. All you nee…

updated 18.0 years ago • Marion Moody

div class="preformatted">You must think that I am pedantic and stubborn ... well, that's me ... I put the pieces together as you painstankingly taught me to do. You...INHBB Therefore my data blocks associate miRNAs with a number of genes 3'UTR regardless of their VALIDATION. Presumably just a subset of all predicted are actually VALIDATED. This is no time or energy wasted because this

miRNA Homo sapiens miRNA Homo sapiens

updated 16.4 years ago • mauede@alice.it

month, the offer of the company that has been co-operating with us for last 14 years. The offer is valid on all the territory of Australia, New Zealand, United Kingdom, Europe. As a leader in the career building, we recommend...account from clients of the comapny. After procedures of transaction documents preparation he/she must transfer the sum to accounts advised by our dispatchers. All you nee…

updated 18.0 years ago • Gonzalo Pelletier

month, the offer of the compnay that has been co-operating with us for last 14 years. The offer is valid on all the territory of Australia, New Zealand, United Kingdom, Europe. As a leader in the career building, we recommend...account from clients of the company. After procedures of transaction documents preparation he/she must transfer the sum to accounts advised by our dispatchers. All you nee…

updated 18.0 years ago • Geoffrey Downs

preformatted">Hello I have data from 5 Illumina mouse 6 beadarray slides. I have read in the bead level data using the beadarray package and used tapply to count the number of beads per probe. As an example, the output below

probe beadarray probe beadarray

updated 18.1 years ago • Krys Kelly

Hello. I was kindly asking how I can convert "Majority protein IDs" to "Gene names" like so: Majority.protein.IDs A0AV96-2;B7Z8Z7;A0AV96;D6R9D6;D6RBS9 A0AVT1;A0AVT1-2 A1L0T0;M0R026 A1XBS5-5;E5RHK0...Hello. I was kindly asking how I can convert "Majority protein IDs" to "Gene names" like so: Majority.protein.IDs A0AV96-2;B7Z8Z7;A0AV96;D6R9D6;D6RBS9 A0AVT1;A0AVT1-2 …

MassSpectrometryData Proteome Database DEP

updated 4.7 years ago • tpm

Hi all, I am using edgeR to identify genes differentially expressed in my experiment. I have cells which were grown in 4 different cell media and I would like to perform an ANOVA to identify DE genes comparing all media vs all (e.g. media1 vs media2; media1 vs media3; media1 vs media4; media2 vs media3....). I have been reading the manual for edgeR and this is my code: ``` > librar…

edger error

updated 6.7 years ago • lucap