Bioconductor Forum

Hi everyone,     I am using genotype.Illumina() in  R packge crlmm to deal with Illumina genotyping data (idat file). However, some errors appear as follows:     <span style="white-space:pre-wrap">cnSet <- genotype.Illumina(sampleSheet=samplesheet, </span><span style="white-space:pre-wrap">arrayNames=arrayNa…

bioconductor

updated 7.1 years ago • junyi

error: Error in makeContrasts(contrasts = "cond0:timePoints- cond1:timePoints", : The levels must by syntactically valid names in R, see help(make.names). Non-valid names: cond0:timePoints,cond1:timePoints Is it the semi

updated 11.4 years ago • Linus Schumacher

other annotation. While parsing back is possible, I assume there's a way to use the original gene name in analysis.</span>   Thanks &nbsp

cummerbund

updated 10.7 years ago • daniel.antony.pass

to put the directory. I try a lot of things and sais this: Error: '\\U' used without hex digits in character string starting ""C:\\U" Error: unexpected input in " miseq\_path <- C:\\"   character(0) Please, I need help, I don´t unsdertand

annotation

updated 8.2 years ago • dra.noika

and use both the weight01 and elim methods for filtering GO terms. I built my gene list as a named numeric vector using all of the genes that were expressed in the data and then calculated a z score to define my genes...log10(de_matrix$padj))), 0.00) ## Make the gene list as a named numeric vector gene_list<-de_matrix$score names(gene_list)<-de_matr…

topGO

updated 20 months ago • adendekk

BSData ExpressionSetIllumina (storageMode: list) assayData: 47293 features, 18 samples element names: exprs, BeadStDev, NoBeads, Detection phenoData rowNames: I.1, IC.1, ..., P42.2 (18 total) varLabels and varMetadata: Sample_Name...BSData ExpressionSetIllumina (storageMode: list) assayData: 47293 features, 18 samples element names: exprs, BeadStDev, NoBeads, Detection phenoData …

Biobase affy affyio beadarray Biobase affy affyio beadarray

updated 19.2 years ago • Keith Satterley

<div class="preformatted">hi, i have found a problem when using the functions addNode() and edgeData() from the graph package, which i believe is a bug and it can be reproduced with the following minimal example: library(graph) ## build a graphBAM object with vertices a, b, d, e and edges a-d, b-e df <- data.frame(from=c("a", "b"), to =c("d", "e"), …

graph graph

updated 12.2 years ago • Robert Castelo

The default options of the function are still leading to the error " sampleNames different from names of phenoData rows" and I am unable to figure out its cause. See below for output and sessionInfo(). It appears to me that the...and rownames of phenodata are identical and I have used setdiff() to verify this (output is character(0) ). Ideas? Thanks, Mark > ReadAffy() Error in validObje…

Biobase affy Biobase affy

updated 19.9 years ago • Kimpel, Mark W

in fitting bioHMM on some non-array CGH data using the function runBioHMM. Say I have have a vector, y, of processed intensity measurements at M SNPs along a chromosome and a vector of corresponding genomic locations

CGH CGH

updated 16.8 years ago • Stacey Burrows

unsigned char),n,instream); #ifdef WORDS_BIGENDIAN /* Probably don't need to do anything for characters */ destination = ~destination; #endif return result; } The assignment destination = ~destination looks bogus to me. And...points to. This probably isn't the right thing to do since we probably don't need to do anything for characters (or char's at least) and this line should be com…

GO makecdfenv GO makecdfenv

updated 20.7 years ago • Cyrus Harmon

and it is defaulted to quote = "\\"". When a queried BioMart field contains a single double quote character, read.table interprets all data that follows that character as a string rather than as the rest of the dataframe...allow users to supply a quote argument of quote = "" when necessary to handle unclosed double quote characters

biomaRt

updated 9.7 years ago • jonathan

<div class="preformatted">I run a heatDiagram and I am with some doubts. First, when I adjust primary=1 in the function heatDiagram, some of the shown genes are different from those shown by the function topTable when I adjust the coef=1. The opposite also happens. (I considered the same amount of genes in both cases). Why? Second, when I adjust primary=2 and I execute the function heatDi…

updated 22.0 years ago • Marcelo Luiz de Laia

library in R library(DECIPHER) # specify the path to each FASTA file (in quotes) # each genome must be given a unique identifier here # for example: Genome1, Genome2, etc. fas <- c(Genome1="<<REPLACE WITH PATH TO FASTA FILE...nbsp;                         &nb…

decipher

updated 8.0 years ago • Vinicius Henrique da Silva

geneList, exponent = exponent, minGSSize = minGSSize, : geneList should be a decreasing sorted vector... Any help in understanding how to 'rank' this in order allow me to run tthe GSEA. I have included my full code below Thank...2", m_t2g$gs_name, perl=TRUE) m_t2g$gs_name <- gsub("Hallmark ","", m_t2g$gs_name) ``` #Now we name genes as the log2foldchange, and names(genes) as the ENTR…

clusterProfiler

updated 3.1 years ago • Rob

<div class="preformatted">Vincent, I am cc'ing the Bioconductor mailing list with the response to your e-mail so others can access it. The gaps,GRanges-method is strand specific, so when you pass a GRanges object containing the transcript bounds into gaps, you will get the gaps on the positive strand, the negative strand, and the both strand category. This is why you found a gap between tr…

TranscriptDb IRanges GenomicRanges TranscriptDb IRanges GenomicRanges

updated 15.5 years ago • Patrick Aboyoun

seqnames ranges strand | gene_id <rle> <iranges> <rle> | <character> AT1G01010 Chr1 3631-5899 + | AT1G01010 AT1G01020 Chr1 6788-9130 - | AT1G01020 AT1G01030 Chr1 11649-13714 - | AT1G01030...these genes are indeed the ones in the warning report ``` > rownames(data)[!rownames(data) %in%…

genomicranges genomicfeatures

updated 5.7 years ago • shangguandong1996

for feature names, correct? I hope the following is clear but if you need more info or context please let me know. Thank you! >raw <- readCtData...48 features, 44 samples Feature types:           Feature names:         PD1 BCL6 BATF ... Feature classes:&…

limma ndups htqpcr software error

updated 10.4 years ago • julio.c.silver

formula with some parameter that I want to minimise with some condition like sum of all of them must be one, in some condition, one of them must equal 0, etc. I am trying to solve that with constrOptim but I got some broblem... Like

updated 13.9 years ago • SimonNoël

which accepts a matrix of PM values. But, normalize.invariantsetdoes not asks for a vector of expression values(x), and another vector of expression values (ref) against which to normalize. Now, does anyone have

Normalization Normalization

updated 21.3 years ago • cchetia@vbi.vt.edu

had much success with 'R' but I am open to any suggestions :) I have two text files containing gene name lists;preferably, I want to be able to simply paste these text files and then have a Venn diagram appear. Does such an online

Venndiagram files text

updated 3.0 years ago • ratto

an annotation package that contains information about features, e.g., maps between (unique) probe names and (possibly repeating) gene names. This is easy for standard chips, since the annotation packages already exist. More...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(labelDescr…

Annotation ExpressionData Annotation ExpressionData

updated 18.5 years ago • Martin Morgan

I want to compute the TMM for two RNASeq-samples in two different conditions. The number of DE genes is different in each sample. In order to compute the TMM normalization is required that the samples have the same genes listed in the corresponding order? If it is the case, how I can do this arrangement? Thanks so much.

TMM edgeR

updated 9.6 years ago • humberto_munoz

One of the changes from DiffBind 1.12.3 to DiffBind 1.14.0 is at line 1045 of analyze.R, where the line: <pre> idx = match(as.integer(sites),1:nrow(pv$allvectors))</pre> in the `` pv.getsites `` function is replaced with: <pre> idx = match(as.integer(sites), rownames(pv$allvectors))</pre> Reading through the rest of the code indicates that `` sites `` is a ve…

DiffBind edgeR

updated 10.7 years ago • Aaron Lun

I am getting an error while mapping the gene names to the StringDB identifiers using the map function. The code was working fine before with the StringDB version 11 but

PPI STRINGdb

updated 4.4 years ago • Ashish Jain

hugo) hugo2 <- as.list(hugo[mapped]) hugoDF <- data.frame(PROBE_ID = as.character(names(hugo2)), SYMBOL = as.character(hugo2))</pre> And the same for  other entries, with later merging them like this: <pre> expressionAnnotationData

probe to gene id illumina beadchip probe quality

updated 9.7 years ago • smt8n

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi), and read those in and transform them to a character vector that looks like GENETIC_CODE. But I realise it might be something useful to have encoded more centrally

VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation

updated 11.9 years ago • Janet Young

Mac with R 3.1.0: > library(BSgenome) > grep("GRCh38", available.genomes(), value=TRUE) character(0) > grep("GRCh38", available.genomes(type="source"), value=TRUE) [1] "BSgenome.Hsapiens.NCBI.GRCh38" Note that in BioC...is the recommended way to lookup a BSgenome object by genome assembly or by full BSgenome package name. If the BSgenome package is not inst…

Cancer BSgenome BSgenome genomes Cancer BSgenome BSgenome genomes

updated 11.8 years ago • Hervé Pagès

extdata",package="GenomicRanges"), recursive=TRUE, pattern="*bam$", full=TRUE) names(fls) <- basename(fls) bf <- BamFileList(fls, index=character()) features <- GRanges( seqnames = c(rep("chr2L", 4), rep("chr2R", 5), rep("chr3L

updated 10.5 years ago • Sang Chul Choi

I have a kalliso-created abundance.h5 file but the filename (ES\_1\_high\_28881\_CGATGT\_abundance.h5) includes information about the sample. When I try to import this file using tximport v1.10.0 I get an error. tximport thinks that the file is a .tsv file.  However, if I create a symlink named abundance.h5, I can load that perfectly well.  Is there a way to tell&…

tximport kallisto

updated 7.0 years ago • Lucas Carey

Treatment + Before + normFactor), the answer is: Error: $ operator is invalid for atomic vectors Based on internet there is  an error when applying `` $ `` to a vector. But how can I fix the problem in the script

fitZig

updated 10.6 years ago • PJ

below result: \[1\] NA Warning messages: 1: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL' Any comments or advice are welcome. Thanks

GOSemSim yeast

updated 10.9 years ago • horcsct

<div class="preformatted">Dear R User, I wrote a simple script in R, just to calculate the sum of the vector ################### New<-function(n,old) { tt=0 k=length(old) for(i in 1:k) { # print(i) tt=tt+old[i] # print(tt) } print(tt) print(n) print(k) if (n == tt){ print ("A--Input is...div class="preformatted">Dear R User, I wrote a simple script in R, just…

updated 13.8 years ago • ALok

agopen() in the C code. JG 02 September 2003: graph - change to edgeWeights() such that weights vectors are now always named. JG 02 September 2003: Imported limma 1.1.14 - read.maimages now supports SMD data files. GKS</div

genefilter affy graph Rgraphviz limma annaffy genefilter affy graph Rgraphviz limma

updated 22.3 years ago • madman@jimmy.harvard.edu

Hi, I have a fastq file named `` fastq1 `` which I upload in R using: `` StreamFastq1=ShortRead::FastqStreamer(con=fastq1,n=2000000) `` `` fastq1yield=ShortRead...Hi, I have a fastq file named `` fastq1 `` which I upload in R using: `` StreamFastq1=ShortRead::FastqStreamer(con=fastq1,n=2000000) `` `` fastq1yield=ShortRead::yield(StreamFastq1) ``   I then use the narrow funstion t…

ShortRead FastqStreamer

updated 8.1 years ago • ioannis.vardaxis

<div class="preformatted">I am using the limma packages for the first time, and I need help with the modifyWeights function. I have about three years of experience with R programing, but this is the first time that I have run an analysis with a bioconductor package. I have included the code below. I know that this is not a reproducible example and I would gladly give any more information…

limma limma

updated 15.9 years ago • stephen sefick

sites from an EPIC array ## all_sites = all sites captured by array ## geneset_collection = named list of format geneset_collection[['pathway1']] = c('entrezID1', 'entrezID2', ...), where entrezID is an entrezID gst_pos <- gsameth...gst_pos[gst_pos$FDR < pathway_FDR, ] Error in gst_pos$FDR : $ operator is invalid for atomic vectors In addition: Warning message: In alias2Sy…

missmethyl gsameth

updated 7.5 years ago • owen.whitley

<div class="preformatted">We are trying to load around 260 cel files in a AffyBatch object. There are 6117 genes in the chip. We tried to load in both Windows and Linux machines. The problem is that we cannot allocate "memory" to load this data. In windows with 512Mb & 4Gb of VirtualMem, we can manipulate the amount of memory available to R but when R process is around 1.6Gb the R…

PROcess PROcess

updated 22.2 years ago • Victor M Trevino-Alvarado

get the following message: Error in as(syn, "MSnSet") :   no method or default for coercing “character” to “MSnSet”   Applying class function to syn, class(syn), returns \[1\] "character" How can I save my data after synergise

synergise synapter

updated 11.1 years ago • sogueta

lt;- go_terms[sapply(go_terms, is_empty_or_na)] # Function to check if a vector of GO terms is valid (not empty, non-null, and non-NA). has_valid_go_terms <- function(go_terms_vector) { !is.null(go_terms_vector...valid_go_terms <- go_terms[sapply(go_terms, has_valid_go_terms)] # Extract the names of genes that have valid GO terms from the db. genes_wi…

GO clusterProfiler enr

updated 16 months ago • Fatima

looks ok (see attached histogram). I have also attached the q value plots and the p value vector for information. Any suggestions why these q values behave the way they do? Greetings Reinhard -- Dr. Reinhard Hoffmann...PUBLIC KEY BLOCK----- -------------- next part -------------- A non-text attachment was scrubbed... Name: ANOVA_p.png Type: image/png Size: 4036 bytes Desc: not available Url : …

updated 20.2 years ago • Dr. Reinhard Hoffmann

gt; I have also tried the following but while my argument is a matrix my output > is a numeric vector that I can't seem to coerce > back into a matrix with the same dimensions I started with. > > > # median normalize all...to be what you want to do. norm.mat <- sweep(s, 2, s.median) As an aside, single letter object names are fine for just playing aroun…

Normalization GO Normalization GO

updated 13.2 years ago • James W. MacDonald

<div class="preformatted">I am using siggenes to do a two class paired analysis of 36 microarrays. I do not appear to have any problems but upon summarizing the results I receive "NA" for fold change. I believe I read somewhere in the vingette that fold change is only calculated for two class unpaired analysis. Is this true? If not, what must I do in order to calculate the fold change i…

siggenes siggenes

updated 17.5 years ago • Mary Winn

color experiment with an Agilent chip. I read the limma User Guide and find out that I must preprocess with the function normalizeBetweenArrays. So I get M- and A-values and my question is which one shows the expression...on the chip Affymetrix Mouse Genome 430 2.0 Array the ID 1449880_s_at stands for three gene names and entrez ids:Bglap /// Bglap2 /// Bglap3 - 120…

RankProd RankProd

updated 11.7 years ago • Stefanie Busch

or physics. A solid foundation in data analysis and programming in a Unix/Linux environment is a must. Knowledge of basic biology is an asset, but is not required. We invite excellent candidates holding a PhD in Bioinformatics...including CV, brief statement of research interests and relevant data analysis experience, names and email addresses of at least 2 referees before November 11th, 2011 …

ASSET ASSET

updated 14.3 years ago • Mark Robinson

27543283 'C:\Users\XXX\AppData\Local\Temp\RtmpO0PFpO\file3a1c3aa8659b' 851 CHR_POS no trailing characters 34150806;34141638 'C:\Users\XXX\AppData\Local\Temp\RtmpO0PFpO\file3a1c3aa8659b' 852 CHR_POS no trailing characters...34141638 'C:\Users\XXX\AppData\Local\Temp\RtmpO0PFpO\file3a1c3aa8659b' 853 CHR_POS no trailing characters 34150806;34141638 'C:\Users\XXX\AppData\Local\Temp\RtmpO0PFpO\file3…

gwascat

updated 4.9 years ago • anailis

the first string it encounters after the ">" sign in a FASTA header and strips away the space character after the string as well as all other characters that come after the space character. In this way you will get any...ID regardless of how it begins with... You only have to check if the space character is OK also in your situation, or if another separator would be more appropriate. Ofter…

probe probe

updated 20.2 years ago • Norman Pavelka

0 8 context direction pValue regionType <character> <numeric> <numeric> <character> [1] CG -1 4.74722531863148e-87 loss [2] CG -1 0.000000000000654240817434598 loss [3] CG -1 1.65931737416942e...and ranges 39 and 40 are duplic…

DMRcaller

updated 6.0 years ago • martin.groth

three factors, but the desgin is unbalanced, so that the tickarks and the lables for the axis are must not evenly distributed. A regular grid via the 'grid' function aligns perfectly with the image cells, but the tickmarks...1:84, x, col=col, xaxt='n', yaxt='n', xlab='', ylab='') # set up the axis > axis(3, i, labels=names(l), las=2, tick=T) > axis(2, i, labels=names(l), las=2, tic…

affy affy

updated 21.5 years ago • Arne.Muller@aventis.com

How can I know the columns accepted when querying a TxDb object? I can explore the columns via `columns` but then other keys are accepted too: ``` r suppressPackageStartupMessages(library("TxDb.Hsapiens.UCSC.hg19.knownGene")) columns(TxDb.Hsapiens.UCSC.hg19.knownGene) #> [1] "CDSCHROM" "CDSEND" "CDSID" "CDSNAME" "CDSSTART" #> [6] "CDSSTRAND" "EXONCHROM" "EXONEN…

TxDb

updated 3.0 years ago • Lluís Revilla Sancho

6 exons. Anything wrong? > > exons <- exonsBy(txdb, "tx",use.names=TRUE) > exons[which(names(exons)=="uc010zum.1")] > GRangesList of length 1: > $uc010zum.1 > GRanges with 6 ranges and 3 metadata columns: > seqnames...ranges strand | exon_id exon_name > exon_rank > <rle> <iranges> <rle> | &l…

ggbio ggbio

updated 11.4 years ago • Tengfei Yin

Warning messages: 1: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 2: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress callback must return boolean 3: In curl::curl_fetch_disk...url, x$path, handle = handle) : progress callback must return boolean 4: In curl::curl_fetch_disk(url, x$path, handle = handle) : progress …

annotationhub dependencies

updated 10.1 years ago • dalloliogm

have a table with expression values for 2000 genes, for 16 samples, rownames are EntrezGeneIDs and a vector which contains the signature, +1 or -1 for 200 genes, names are EntrezGeneIDs. >> So I wanted to get the activity scores...have a table with expression values for 2000 genes, for 16 samples, rownames are EntrezGeneIDs and a vector which contains the signature, +1 or -1 for 200…

DART DART

updated 11.9 years ago • Lawler, Katherine

Hi, I am currently using the DEseq2 package to carry out differential gene expression. When i try to drop levels it gives me an error message saying " no applicable method for 'droplevels' applied to an object of class "character". Can you please explain how I can fix this please? Also I would like some more info on the function 'droplevels' and how...me an error message saying " no applicabl…

droplevels DESeq2

updated 4.0 years ago • bjen731

250 0 T N depth bam <integer> <integer> <numeric> <character> [1] 0 0 250 CleanedBams/FLD0097.bam [2] 0 0 251 CleanedBams/FLD0097.bam [3] 1 0 252 CleanedBams/FLD0097.bam I think that...case that the applyPileup function is using the same limit, and i…

Sequencing ggbio Sequencing ggbio

updated 13.1 years ago • Mark Dunning

<div class="preformatted">I am reposting to the mailing list as it was bounced the first time. Sorry if you received this more than once. Best, Norman ---------- Forwarded message ---------- From: Norman Pavelka <normanpavelka@gmail.com> Date: 2011/9/22 Subject: Re: Help on PLGEM R Package Data Import To: Wu Qi <qwu at="" dicp.ac.cn=""> Cc: bioconductor at stat.math.ethz.ch, m…

Biobase plgem Biobase plgem

updated 14.3 years ago • Norman Pavelka

o a matrix of data(24136, 28). the error is the following. normalize.loess(matrix) Error in vector("double", length) : vector size cannot be NA it is strange, because it do not happen if I subindex the matrix for less genes

updated 19.1 years ago • claudio.is@libero.it

div class="preformatted">Hi, I have a vector x of length = 2109199 The coordinates are from 50 to 146273025 (approximately every 35bp, but there are some gaps) I set...Error in .Call("findsegments", G, maxseg, verbose, PACKAGE = "tilingArray") : negative length vectors are not allowed Help anyone? Thanks! -HT [[alternative HTML version deleted]] </div

updated 16.8 years ago • Hui Tang

div class="preformatted">Hi, I have a vector x of length = 2109199 which I want to segment using the function segment() in package tilingArray. I set the two parameters...Error in .Call("findsegments", G, maxseg, verbose, PACKAGE = "tilingArray") : negative length vectors are not allowed Help anyone? Thanks! -HT [[alternative HTML version deleted]] </div

tilingArray tilingArray

updated 16.8 years ago • Hui Tang

lt;- dist(typVSN, method = "euclidean", diag = FALSE, upper = FALSE) Error: cannot allocate vector of size 589776 Kb > typVSNcluster <- hclust(dist(typVSN@h)) Error: cannot allocate vector of size 589776 Kb I'm running

updated 22.8 years ago • Jason Skelton

package = "seqinr") cc<-read.fasta(file = dnafile) cc gives me then the following vector ... [47764] "t" "c" "c" "c" "t" ...... My problem is I would like now to use that vector to perform basic statistics eg; GC content analysis, base...frequencies . I hardly see how ? For instance an histogram on my vector like hist(cc) don't work My first intention by the way was to use biostring …

updated 16.2 years ago • m a