Bioconductor Forum

I'm using Deseq2 for differential gene expression analysis and then for downstream analysis i'm going to classify healthy vs disease states using support vector machine. The data comprises of healthy and disease states which sequenced in 13 batches. I have 2 questions: 1) I used...and then for downstream analysis i'm going to classify healthy vs disease states using support vector machi…

deseq2 batch effect classification

updated 7.3 years ago • Maryam

<div class="preformatted">Hello, This question isn't about profilePlots in particular, but about subsetting a vector by a set of values. > Top25Expr[which(annoT[,"symbol"]==as.character(peak[1,]) | annoT[,"symbol"]==as.character(peak[2,]) |annoT[,"symbol"]==as.character(peak[3,]) | annoT[,"symbol"]==as.character(peak[4,]) | annoT[,"symbol"]==as.character(peak[5,]) | annoT[,"symbol"…

updated 13.4 years ago • Dario Strbenac

Hello, I recently downloaded CRISPRSeek and I got the tests to work in the vignette (specifically Scenario 5: Target and off-target analysis for user specified gRNAs) and the output looks wonderful. When I tried to replicate the results with a test file on my own, however, I got the error as described in the post title. Here is the following code that I ran: <pre> library(CRISPRseek) li…

CRISPRseek

updated 8.4 years ago • robert_w_link

environment consisting of multiple and changing priorities, under stringent deadlines. The candidate must also have sound judgment, pay close attention to detail and be completely dependable, reliable, and trustworthy. Preferred...at https://jobs.illinois.edu, directly apply to our position and upload cover letter, resume, and names/contact information for three references by April 6, 2022. Onlin…

Metabolomics

updated 3.8 years ago • Jenny Drnevich

ti <- matchPDict(DNAStringSet("GC","CG"),tdna) Error in .normargSEW(start, "start") : 'start' must be a vector of integers > sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under

Biostrings

updated 7.6 years ago • Brian Smith

The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. ``` Does biomaRt not support multiple IDs matches now

annotation

updated 6.1 years ago • giotto_gui

aqm_raw' has been created. Error in `sampleNames<-`(`*tmp*`, value = NULL) : number of new names (0) should equal number of rows in AnnotatedDataFrame (2) Error in obj[[i]]$legend : $ operator is invalid for atomic vectors In

arrayQualityMetrics arrayQualityMetrics

updated 16.2 years ago • Joern Toedling

I've followed directions from a previous post and have managed to get good results. The thread is named "edgeR: finding tissue specific genes" and here is the link: http://permalink.gmane.org/gmane.science.biology.informatics.conductor...time creating the contrast for the last tissue in limma. For the last tissue, the contrast is a vector with 18 elements which lmFit does not like. First of all,…

RNASeq limma edgeR RNASeq limma edgeR

updated 12.6 years ago • Jaaved Mohammed

and then call the next fasta and run through the full list of files again while outputting relatable names? The idea would be that parameter 1 would concur with fasta1, MSGFplus would run through the samples, produce mzid files

MSGF+ Proteomics r

updated 6.3 years ago • laural710

What kind of argument must be entered so I can choose the x and y limit when calling the plotGate() command

flowworkspace

updated 8.5 years ago • justinyi10

<span style="line-height:1.6">I'm trying to use the analyzeFeatures function in SGSeq following the vignette, but I get this error:</span> > library(SGSeq) > library(TxDb.Hsapiens.UCSC.hg19.knownGene) <span style="line-height:1.6">> sgfc <- analyzeFeatures(bam.info, which = gr)</span> Predict features... <span style="line-height:1.6">…

SGSeq

updated 10.5 years ago • Helen Zhou

sorted and indexed. It shows error: Error in .normarg_totalsize(totalsize) : 'totalsize' must be a single integer My code is pasted below: ``` > library(QuasR) > library(BSgenome) > library(Rsamtools) > library(rtracklayer...collecting quality control data Error in .normarg_totalsize(totalsize) : 'totalsize' must be a single integer ``` Any su…

QuasR qQCReport QuasR error Error in .normarg_totalsize(totalsize)

updated 6.0 years ago • A.Singh

in `collect()`: Failed to collect lazy table. Caused by error in `db_collect()`: Arguments in `...` must be used. Problematic argument: ..1 = Inf Did you misspell an argument name? Run `rlang::last_trace()` to see where the error occurred

getBM biomaRt

updated 2.1 years ago • ai.yaku

graduate levels, and participate in departmental and interdepartmental graduate programs. Applicants must hold a PhD and one year of postdoctoral experience is preferred. The deadline for receipt of applications is January...2) a statement of research interests, and (3) letters from three references (Assistant Professor) or names of three references (Associate or Full Professor) to: Guille Baca,…

updated 18.2 years ago • Thomas Girke

<div class="preformatted"> [NOTE RELEASE DATE CHANGED TO 26 April] 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...packages please send me an e-mail with co…

Biobase annotate edd genefilter geneplotter rhdf5 multtest ROC tkWidgets affy AnnBuilder

updated 23.8 years ago • Vincent J. Carey, Jr.

matrix(ncol=96,nrow=0) for(i in list_vcf) { vo = readVcf(i, "hg19") # sample name (should pick up from the vcf automatically if available) # colnames(vo) = i m0 = genCountMatrixFromVcf("BSgenome.Hsapiens.UCSC.hg19...fdef, mtable) : unable to find an inherited method for function ‘getSeq’ for signature ‘"character"’ Has anyone come across the same prob…

signeR getseq

updated 6.7 years ago • TRASA

seqnames strand cigar qwidth start end width <rle> <rle> <character> <integer> <integer> <integer> <integer> [1] seq1 + 35M 35 36 70 35 [2] seq1 - 35M 35 185 219 35 njunc <integer> [1] 0 [2] …

GenomicAlignments

updated 3.0 years ago • Robert Castelo

all five shuffled sets ## this gives "with_shuf12345" # also repeat, but after giving unique names to each of the shuffled sequences in the background set ## this gives "with_shuf12345n" # Combine the results for the top...motif target.hits target.seq.hits target.seq.count bkg.hits bkg.seq.hits bkg.seq.count Pval <character> <integer> <integer> …

universalmotif scanning enrich_motifs PWM

updated 4.0 years ago • alexandre.blais

I have three types of samples PC3M (the control cell line), Knockdown (PC3M with an siRNA knockdown vector) and Scramble (PC3M with a vector with a scrambled sequence). I have set up my design matrix like this: design <- modelMatrix

Cancer Cancer

updated 17.3 years ago • Daniel Brewer

gt; on the slide which are to be removed. In the marrayLayout there is a slot > "maSub" (logical vector) where one can define the good spots. > Besides, when you print the features of your slide there is a line : > > "Currently...seem to > take the subset into account even when you fill the field 'subset' with > the 'maSub' vector. > > It se…

Microarray Normalization Microarray Normalization

updated 21.8 years ago • anthony.ferrari@ensimag.imag.fr

the accessor function 'cellAssignments()' on the 'CyData' objects, which returns a list of integer vectors containing the cell IDs/indices of the cells contained within each hypersphere. This allows the individual cells...level q-values. However, I noticed that some of the values in these 'cellAssignments' integer vectors are actually negative, which doesn't seem to make sense if they are cell I…

cydar

updated 8.5 years ago • Lukas Weber

RG.all contains all the data you wish to compare, you only need to pass this data.frame along with a vector of classlabels that identify which class each column of data belongs to. If you are doing a two-class unpaired analysis...this will be a vector of 0s and 1s. If paired, then paired integers from 1:n, and if oneclass, a vector of 1s. HTH, Jim James W. MacDonald Affymetrix

Microarray Cancer siggenes Microarray Cancer siggenes

updated 22.1 years ago • James W. MacDonald

<div class="preformatted"> Hi, I suspect this is something to do purely with my connection, but I thought I'd ask, just in case: I have a list of refseq ids (NM_xxxxx), 18028 of them. I wanted to get the gene symbols for those genes, so I used biomaRt on the whole list. What I got was a single column data frame longer than 18028, as I get multiple results with some of these refseq ids. Th…

GO biomaRt GO biomaRt

updated 19.4 years ago • J.delasHeras@ed.ac.uk

hypergeometric analysis ... Error in as.vector(x) : no method for coercing this S4 class to a vector my gsca object can be downloaded from : http://129.94.136.7/file_dump/dario/gsca.obj > head(scores) 643837 148398 339451...1] "55966" "249" "2048" "9473" "80149" "353500" Also, it would be nice if the hits vector isn't mandatory. Figure 1 of the vignette says the packag…

HTSanalyzeR GSCA HTSanalyzeR GSCA

updated 14.2 years ago • Dario Strbenac

<div class="preformatted">Hi, I am analyzing a matched pair tumor/normal rna-seq data set. After aligning with bowtie2 against UCSC hg19 index, I am trying to get the counts for each of the samples using the iGenomes UCSC GTF file. I came across the following tutorial which shows different ways to do it in Bioconductor: http://faculty.ucr.edu/~tgirke/HTML_Presentations/Manuals/Workshop_D…

updated 11.7 years ago • Pankaj Agarwal

2. Get an expression matrix of mapped probes mappedProbes <- sort(which( (probNames %in% names(gMap1)) == T)) any( mappedProbes != sort(mappedProbes)) # FALSE notMappedProbes <- which( (probNames %in% names(gMap1)) == F) mappedNames...lt;- as.character(gMap1[ which(names(gMap1) %in% rownames(expr.matrix)[mappedProbes]) ]) rownames(expr.matrix)[mappedProbes] <- mappedNames ex…

annotate affy convert oligo annotate affy convert oligo

updated 12.6 years ago • Ranjani R

data for features identified with Ensembl transcript IDs. The ExpressionSet constructor wants a character string for annotation data. Is there another way to populate the slot? From an AnnotatedDataFrame? Should I write

updated 17.3 years ago • Michael Muratet

and "hsTargets" and noticed that none of the miRNA identifiers in dataset "hsSeqs" contains the character "*" whereas many miRNA identifiers in dataset "hsTargets" end with the character "*". I checked a couple of them and found

miRNA miRNA

updated 16.3 years ago • mauede@alice.it

Hello! I am using ChIPseeker to analyze the BED data from SEACR (a CUT & RUN analysis tool). When I used readPeakFile() function in ChIPseeker to read the BED file, it gave out such a list: ##GRanges object with 18965 range and 3 metadata columns: ## seqnames ranges strand | V4 V5 V6 ## <rle> <iranges> <rle> | …

ChIPseeker

updated 5.3 years ago • ahua217

lt;Rle> | <factor> <DNAStringSet> <CharacterList> <numeric> <character> DEL00119550 1 [ <span style="background-color:Yellow"> 9903713, 9903713</span>] * | <NA> N <DEL> <NA> PASS DEL00139228...END …

VCF iranges End software error variantannotation

updated 11.1 years ago • tiffanie.moss

Error in mergeScores(merged, def, peakset, TRUE) : Not compatible with requested type: [type=character; target=double]. > sessionInfo() R version 4.2.0 (2022-04-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under

DiffBind

updated 3.6 years ago • niimabear

error: .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name. I thought it might be because I mistakingly did not have unique column names, but I couldn't find a problem with it. Then I...in .deriveTableNameFromField(field = keytype, x) : Two fields in the source DB have the same name. ``` if anyone can help, I will ver much appreciate it. Tal &…

software error go AnnotationForge AnnotationDbi

updated 6.0 years ago • tzaquin

error: Removing intercept from test coefficients Error in data.frame(logFC = M\[top\]) : row names contain missing values traceback() 4: stop("row names contain missing values") 3: data.frame(logFC = M\[top\]) 2: .topTableT(fit = fit

limma

updated 7.6 years ago • owen.whitley

<div class="preformatted">This is somewhat related to this question, I just want some more clarification on using the CNA function. This is probably very elementary, I apologize in advance https://stat.ethz.ch/pipermail/bioconductor/2007-September/019138.html >From an agilent data set the SystematicName column is composed of elements of the form chr3:175483690-175485000. So for exa…

DNAcopy DNAcopy

updated 11.5 years ago • Nikolas Balanis

rows and the first value is not 7105, showing that the query is not happening by order in the filter vector and I am getting too many hits, with doubled lines with almost the same information, and not by the order of the query...vector (see result below), can someone, help me with this? head(test3) ensembl_gene_id entrezgene hgnc_symbol 1 ENSG00000198692

updated 16.1 years ago • Andreia Fonseca

<div class="preformatted"><kfbargad at="" ehu.es=""> writes: > Dear list, > > sorry for this very basic question but I have searched the R manual > without success. What function do I need to randomly split a > data.frame into two data.frames (for example a data.frame containing > 200 rows and 5 columns into two of say 150 and 50 rows each)? …

Cancer Cancer

updated 18.7 years ago • Seth Falcon

I consistently get the error: Error in t(design) %*% design : requires numeric/complex matrix/vector arguments For example, if I run: model = model.matrix(~as.factor(Sex) + as.numeric(Age)) ComBat_dat = ComBat(gene_express...s) Standardizing Data across genes Error in t(design) %*% design : requires numeric/complex matrix/vector arguments However, when I use a model that only includes fac…

sva sva

updated 12.0 years ago • Jordan Ramsey

_IDs %in% DE\_genes\_Grade  all\_genes <- factor(as.integer(inSelection\[in\_universe\])) names(all\_genes) <- gene\_IDs\[in\_universe\] ont <- "BP" top\_Grade\_GO\_data <- new("topGOdata", ontology = ont, allGenes = all\_genes...annFUN.db, affyLib = "hugene10sttranscriptcluster.db") Error in .local(.Object, ...) : allGenes must be a factor with 2 l…

topgo

updated 8.3 years ago • peirinl

25,25,26,26,27,27, + 28,28,29,29,30,30,31,31) > #extract out the names of the BAM files > #to the bamFls variable (character variable) > bamFls <- list.files(path="bamFiles/", + pattern="bam$", full...sub("\\..*", "", basename(bamFls))))] > #Assigning names to each data in …

summarizeoverlaps summarizedexperiment count matrix low counts rna-seq

updated 9.9 years ago • shania90.lk

<div class="preformatted">There was no attachment with your message and I often think that's a good thing... I rather have the description of your environment and commands that you tried in the body of the email. Regardless, using R-2.14.1, I ran the commands that the vignette suggested using the MLL.A and everything worked as expected... but you have to open the file index.html with your …

Preprocessing arrayQualityMetrics Preprocessing arrayQualityMetrics

updated 13.9 years ago • Benilton Carvalho

This function loads a BED-like file and stores it as a GRanges object. # The tab-delimited file must be ordered as 'chr', 'start', 'end', 'id', 'score', 'strand'. # The minimal BED file must have the 'chr', 'start', 'end' columns. # Any columns after the...3 columns") } header <- c('chr','start','end','id','score','strand') names(df) <- header…

ggbio ggplot2 legend bioconductor karyiogram

updated 9.3 years ago • oswaldo.lorenzo

percent.mito UMAP_1 UMAP_2 seurat_clusters integrated_snn_res.0.8 integrated_snn_res.0.5 <character> <numeric> <integer> <numeric> <numeric> <numeric> <factor> <factor> <factor> C21_AAACCCACACCCTCTA-1 C21 4409 1837 4.76298...reacreate.partition<-c(rep(1,length(cds@colData@row…

SpecificClusters TrajectoryAnalysis PseudotimeAnalysis Monocle3

updated 3.6 years ago • martacrespi7

of the sample, and with cDNA probes spotted on the membrane. We do first an hybridisation with a vector oligonucleotide, that match all spot on the chip. This is to adjust for the different quantities spotted on the chip...use it in limma. In this function, R channel correspond to the complex set, and G channel to the vector set. (two successive hybridisations on the same membrane). But in fact…

affy limma oligo affy limma oligo

updated 20.2 years ago • TEXTORIS Julien

is my code and all I get is an empty list. This empty list is under the title "Values" and it is a "character (empty). ```r goID <- "GO:0003677" gene.universe <- genes(GOdataUp.res2.2) go.genes <- genesInTerm(GOdataUp.res2.2

topGO

updated 3.9 years ago • Noy

gt; showMethods('readFastq') Function: readFastq (package ShortRead) dirPath="SolexaPath" dirPath="character" -- Regards, Peng </div

updated 15.7 years ago • Peng Yu

tx_id tx_name <rle> <iranges> <rle> | <integer> <character> ENSMUST00000193812.1 chr1 3071253-3073452 + | 1 ENSMUST00000193812.1 ENSMUST00000082908.1 chr1 3100016-3102215...as an extra column in the metadata. Could you please help me figure out how to do so? Thank you!!</character></…

TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus

updated 23 months ago • ramonmassoni

unique regions... Number of unique short reads: 19523016 Calculating genomic coordinates...Error in vector(length = supersize_chr[length(chromosomes)], mode = "character") : vector size cannot be NA/NaN ________________________________...provider: Phytozome (JGI) | provider version: 3.0 | release date: January 2010 | release name: Populus trichocarpa v3.0 | | single sequences (see '?seqnames')…

Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS

updated 12.1 years ago • Vining, Kelly

fdef, mtable) : unable to find an inherited method for function ‘annotation’ for signature ‘"character"’ My `sessionInfo()` are: R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64...inherited methods; didn't return a unique method", domain = NA) })(list("character"), new("standardGeneric", .Data = funct…

cross meta-analysis crossmeta

updated 4.9 years ago • michael.s

267375_at", "267457_at", "267477_at", "267555_at", "267639_at", "AFFX-r2-At-Actin-M_s_at" ), .Names = c("245062_at", "245107_at", "245137_at", "245178_at", "245189_at", "245305_at", "245339_at", "245381_at", "245392_at", "245411_at", "245412_at...When I run this and do probeSetSummary2(posss8) I get the warning message: Warning message: The vector of geneIds used to create the GOHyperGParamsobj…

GO ath1121501 GO ath1121501

updated 12.2 years ago • Guest User

<div class="preformatted">Hi, I have just started working with VCF files and have discovered the VariantAnnotation package, many thanks for making these functions available. Following the code outlined in the reference manual for MatrixToSnpMatrix, my VCF returns only NA values: > head(geno(vcf)$GT) GHS008 GHS015 GHS025 GHS026 GHS027 GHS031 GHS033 GHS034 GHS036 chrM:73 …

updated 13.0 years ago • Lavinia Gordon

from ENSEMBL ID. The following function work for HGNC symbol but I failed to retrieve vgnc gene name. <pre> add.anns <- function(df, mart, ...) { nm <- rownames(df) anns <- getBM( attributes = c("ensembl_gene_id", "hgnc_symbol","vgnc_genename...lt;- nm df }</pre>   Can you  tell me if there is an attribute to obtain vgnc gen…

biomart mart getbm

updated 7.5 years ago • cagenet34

me as I explain what's going on. I'm using IRanges and trying to subset an IntervalTree using a vector of indices found from an ``overlap`` query. R doesn't like this and behaves as if the variable I'm using to subset my IntervalTree...diff(start(ir[hits])) } else { NA } }) The problem is that R somehow thinks the ``hits`` vector is non- existent when I'm trying to use it to index th…

Cancer IRanges Cancer IRanges

updated 16.4 years ago • Steve Lianoglou

Hello, I'm attempting to run a glm analysis with edgeR on 32 biologically independent samples, with 3 factors. I have sex, age, and genotype. I'd like to create a full design matrix, but I'm having some trouble doing this, and understanding all the contrasts possible. <pre> > sex = rep(c("m","f"),each=2,times=8) > time = rep(c("p0","p2","p6","p12"),each=8) > geno = …

edger glm rnaseq

updated 8.1 years ago • Denniswu

different from IntegerList. However, I tried other way like such as coercing IntegerList to integer vector then use `` unique ``, or `` duplicated ``method, but if I do this way I could have `` NA ``instead (`` NA `` shouldn't be in IntegerList). Because...hitTB, order of IntegerList is different, I intend to manipulate them as follows: <pre> idx <- names(hitTB_1) hitTB_1 hitT…

r iranges integerlist

updated 9.3 years ago • Jurat Shahidin

system elapsed 3.084 0.000 3.125 Another odd behavior is that if the query contains sequence names not contained in the subject an error is raised the other way around works fine. Wouldn't it make sense so set the vector

updated 14.8 years ago • arne.mueller@novartis.com

Hello all, as a disclaimer, I am new to array analysis, having started this week, however I cannot find a solution and suspect I must be doing something wrong, so I have resorted to making my first post. My problem in particular is that I see abnormally high...I am new to array analysis, having started this week, however I cannot find a solution and suspect I must be doing something wrong, so I…

limma p values microarray illumina

updated 10.0 years ago • Jason

nbsp;                           names                 \[1\] 594102056 CTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCCTAACCCTAAACCCTAACCAAAACCCTAAACCCTAAACCCCTAAACCCTAAACCCTAACCTAA...test\_2bit\_out) Error …

BioStrings rtracklayer

updated 7.3 years ago • saripalligautam86

error in evaluating the argument 'x' in selecting a method for function 'nrow': Error: no slot of name "elementMetadata" for this object of class "GenomicMethylSet"</pre> In the following instance, I attempted to load an .Rdata...error in evaluating the argument 'x' in selecting a method for function 'nrow': Error: no slot of name "elementMetadata" for this object of class "GenomicMethylSe…

minfi

updated 10.2 years ago • maden.sean

gt; summary(model.full_nodye) Length Class Mode probeid 43381 -none- character yhat 2082288 -none- numeric S2 173524 -none- numeric loops 43381 -none- numeric S2.level 3 -none- character G 43381 -none...numeric Array 1041144 -none- numeric Array.level 24 -none- charact…

maanova oligo maanova oligo

updated 15.9 years ago • Maciej Jończyk

However, "apeglm" requires the use of 'coef' and I've not been able to find a way of creating the name or finding the number of the coefficient for the above contrast. Please could anyone help me out with this? Many thanks

deseq2 lfcShrink apeglm

updated 6.1 years ago • coulsonr