Bioconductor Forum

warnings() Warning messages: 1: In start(ranges(x1Split[[st]])) - end(subSplit2) : longer object length is not a multiple of shorter object length 2: In start(ranges(x1Split[[st]])) - end(subSplit2) : longer object length is not a multiple...of shorter object length 3: In start(ranges(x1Split[[st]])) - end(subSplit2) : longer object length is not a multiple of shorter object length 4: In st…

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

a full model to one with simply an intercept, and with that I end up getting ~20k DE genes – essentially everything that has a non-zero expression at some point. What I did then was extract the parameter estimates...and intercepts for the model, and then filtered the genes for what had a max predicted counts lower than 10 and logFC of 2 within the time frame of each genotype. This filtering...ste…

deseq2 timecourse multiple time points mlr michael love

updated 7.6 years ago • ap874

preformatted">Hi, I want to iterate over an RNAStringSet (rs) to do a calculation for each of the sequences in the form of: 1) get the sequence 2) do the calculations 3) plot the results and 4) use the sequence name (names(rs) in plot...library("Biostrings") rs = read.RNAStringSet('test.fa') R> rs A RNAStringSet instance of length 4 width seq …

updated 13.5 years ago • Kemal Akat

I'm using limma package to count differential gene expression. I need to make a table of logFC of genes specific for my cells of interest (there are 62 of them). What should I write...to make such a table (where should I place the names of the genes)? My code at the moment: Code should be placed in three backticks as shown below ``` gset <- getGEO("GSE24742", GSEMatrix...TRUE, AnnotG…

DifferentialExpression limma R TissueMicroarrayData

updated 3.0 years ago • Элина

HI, I got a SummarizedExperiment file and would like to extract gene expression for further analysis. However, there is no name for the assay, how I can change the name or subset data. Thank you...rownames(15093): ENSG00000000003 ENSG00000000419 ... ENSG00000273488 ENSG00000273489 rowData names(3): Ensembl_ID GeneID EntrezID colnames(100): 1 2 3 ... 99 100 colData names(14): nu…

deseq2

updated 5.5 years ago • georgina.fqw

Hello, I have another problem with biomaRt. My ranked list of differentially expressed genes (ENSG...) are not ordered by the id number but by the expression fold change (naturally): __> library(biomaRt) > mart <- useMart...9  ENSG00000132109 10 ENSG00000140090 But after I used getBM function to get the gene names for the list: __> res <- get…

biomart ensembldb error

updated 7.9 years ago • Yuqia

span style="line-height:1.6">Hi, </span>     Im working with a 53 sample of OTU sequences and I was hoping to create a new MRexperiment with a subset of the samples. I would like to use the sample name as the...create a new MR experiment. but I can only achieve to get one sample at a time using the sample name, so I go from : _MRexperiment (storageM…

metagenomeseq

updated 10.5 years ago • rleonzay

nbsp; <pre> > mae2 A MultiAssayExperiment object of 5 listed experiments with user-defined names and respective classes. Containing an ExperimentList class object of length 5: [1] BRCA_miRNASeqGene-20160128: SummarizedExperiment

multiassayexperiment

updated 7.4 years ago • mario.zanfardino

do some moderated t-test differential testing on with limma. In this data, many of the reads have sequenced through into the poly(A) tail, and we believe this gives us information about changes in poly(A) tail length. For each...gene and sample, we can calculate an average observed tail length. It seems easy enough to calculate a standard error for this...meaning in terms of measurement variance…

limma limma

updated 11.6 years ago • Paul Harrison

Francks, investigates the genetic basis of human brain lateralization using techniques including RNA sequencing, whole exome and genome sequencing, and genome-wide association scanning. Language depends on left-lateralized...Language & Genetics Department uses state-of-the-art methods to trace the connections between genes, neuronal and brain functions, and behavior. We benefit from close…

job rnaseq rna-seq genomics data integration Job

updated 10.3 years ago • clyde.francks

PI positions. *Our research* Our research takes a genomic, integrative approach to understand gene regulation and evolution. We use datasets including genome sequences, gene expression, ChIP-seq, iCLIP and HiC data to...gain insights into: 1) How gene expression is controlled; 2) How this system regulates biologically important behaviours; 3) And how a breakdown in this...of chromosomes in the n…

Cancer genomes Cancer genomes

updated 12.8 years ago • Kathi Zarnack

mailing list. According the a survey of bioinformaticians collected this year, R is now the most popularly used language in bioinformatics. Details here: http://bioinfsurvey.org/analysis/programming_languages

updated 13.8 years ago • Guest User

Hi, I'm struggling to figure out how to go from gene expression data to  be able to create a network out of the most expressed genes in a cell line. Ok, I have developed an...samples in this [dataset](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32474). 2: Use the most expressed genes in the NCI\_H23 cell line to create a subnetwork using a protein interaction network database …

gene expression network cytoscape

updated 8.0 years ago • torgeirous

symbol 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...values = nm, mart = mart) anns <- anns[match(nm, anns[, 1]), ] colnames(anns) <- c("ID…

biomart mart getbm

updated 7.5 years ago • cagenet34

pre> expression <- cbind(expression, rrM.ProfileData)</pre> The following is my function genes is a character vector containing names of the desired genes. cancer is also a character vector string containing names...numeric", length=length(genes)) for(i in 1:length(genes)){ Expression[i] <- cfunc(as.vector(Metastatic.Prostate.Cancer.ProfileData[i...Metasta…

loop matix

updated 10.0 years ago • Arman Shahrisa

are right about alternating write and writeFASTA to access the same file. I was asked to separate sequences by an empty line, which would spoil the FASTA format. Therefore now I do not use write any more. Just writeFASTA. Thank...gt; I realize function write FASTA expects a list with two items, > respectively, description and sequence. > However, just passing a list won't work (ple…

Biophysics Biophysics

updated 16.5 years ago • mauede@alice.it

I am looking to use customproDB with my bam files, vcf and gene fusion data to generate custom peptide sequences. I am particularly interested inbcr gene fusion events. I was going...through the documentation and was not quite sure how to represent my gene fusions in the bed file so that they will be picked up by the software based on the categories in the JunctionType labels

fusion bed files gene fusion bed file

updated 9.9 years ago • ramaniak

Rle objects bf = BamFile(bam, asMates = TRUE, qnameSuffixStart = ".") tx_compat_cvg=RleList() genes=all_genes[unlist(runValue(seqnames(all_genes)))==ch] gr = as(seqinfo(bf), "GRanges") if(ch %in% runValue(seqnames(gr))){ param = ScanBamParam...gal2))==FALSE] grl <- as(gal2, "GRangesList") gal3=reduce(grl) #only keep genes on the current c…

DegNorm GenomicAlignments

updated 3.7 years ago • Jiping Wang

<div class="preformatted">Dear BioC What is currently considered the best method of normalisation where the assumption that most genes are unchanged is invalid? Is it best to apply the Li & Wong algorithm or are there other methods that I should consider? I wish to normalise and analyse the following: 1. A focussed oligonucleotide array. Although this included a good number invari…

updated 21.4 years ago • Aedin Culhane

Currently, I am analysing sc-RNA sequencing data. As far as I know, there are several normalization methods available when differential gene expression analysis...is performed. However, in my case, I have a predefined set of genes (n=530), and I want to compare the expression of these genes between different kinds of cells (intersample comparison). To...so CPM should do that trick. But I do no…

RNA seq cpm

updated 5.8 years ago • isabel.pieterse

I am reading about a new package and I am interested in plotting logo of a protein sequence. The problem is that the author did not specify how one can convert the sequence to number https://www.bioconductor.org...packages/devel/bioc/vignettes/motifStack/inst/doc/motifStack_HTML.html#plot-an-amino-acid-sequence-logo Here is an example sequence seq <- "MGLRYSIYIENPLSSPSSSYKS…

motifStack

updated 6.8 years ago • Bioinformatics

GenomicAlignment and DEseq2 to analyse RNAseq expression. Now I want to calculate one known fusion gene expression in my two RNAseq samples which are from cancer cells that I know have the fusion gene. So I know this fusion gene...sequence, but I have no idea how to count the reads coverage falling on this fusion sequence. Can you help, many thanks in advance

fusion genes rnaseq

updated 10.8 years ago • stephen66

I have a very small shRNA-seq screen dataset that contains only 36 shRNAs (targeting a total of 17 genes) with one shRNA being a control (i.e. no change in its representation is expected over time). Most of the other shRNAs targeting...genes that are thought to be essential for cell survival. It is a time course experiment with two replicates for each time points...examples provided in http://bio…

edger shrna

updated 8.9 years ago • sirintra

I have recently carried out a stipple sequence alignment using DECIPHER package in R. The code was fairly simple as follows: bod\_aa <- readAAStringSet("BOD\_aa.fasta...the percent homology between the different proteins? If possible percent homology to one of the sequences in particular. I.e. I really want to align all the sequences to one "query sequence" and get a percent homology to t…

decipher r protein alignment

updated 7.7 years ago • reubenmcgregor88

<div class="preformatted">Hi Steffen, I encountered the following error while trying to obtain the sequence using archived sequence data from Zv7. Your help is greatly appreciated. Best regards, Julie mart <- useMart(biomart="ensembl_mart_51", dataset="drerio_gene_ensembl", archive=TRUE) Checking attributes ... ok Checking filters ... Ok seq1 = getSequence(id = "ENSDARG000000545…

updated 16.5 years ago • Julie Zhu

from the paper: A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data http://nar.oxfordjournals.org/content/38/3/e17/F1.expansion.html If not, can someone shed some light...from / citation of how it was redone? \* I am looking to map the probe IDs to ensembl transcript names, not just the gene names. The package doesn't have this informat…

microarray annotation illumina human ht-12 v4

updated 10.2 years ago • VSM

nbsp;   0   <a name="86137"></a> [![gravatar for tarek.mohamed](https://secure.gravatar.com/avatar/a1153976bb5d406f3002a65f0ece23fe?s=82&amp...analyzed using DESeq2. I got this error __Error in if (is.na(index) || index < 0 || index > length(nd)) stop("vertex is not in graph: ",  :    missing value where TRUE/FALS…

topgo rnaseq

updated 9.4 years ago • tarek.mohamed

TCGA data and doing the differential expression analysis for about 6,000 samples and 20,000 coding genes. I was suggested to use DESeq2 for DE analysis, but the DESeq() takes an extremely long time with 6,000 samples, therefore...packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html), the scaled counts generated from abundance ("scaledTPM" or "lengthScaledTPM") are recommended to be used…

tximport limma deseq2 differential expression

updated 7.4 years ago • mico

<div class="preformatted">Bioconductors! Please join us for an intermediate course on use of R / Bioconductor for high-throughput sequence analysis, a brief outline of which is below. More Information: https://secure.bioconductor.org/Seattle-May-2013/ Intermediate...Please join us for an intermediate course on use of R / Bioconductor for high-throughput sequence analysis, a brief outline …

Cancer Cancer

updated 12.7 years ago • Martin Morgan

non-model plant species, and used the Salmon -> tximport -> DESeq2 analysis pipeline. For the most part the leaf data looks pretty good. However, I have come across an interesting issue when it comes to the dry seed data...last seed time point). Although most genes are not DE (based on DESeq2), the vast, vast majority of reads are mapping to just a few DE genes. Over 50% of counts …

rnaseq deseq2

updated 7.5 years ago • Poikilo

<div class="preformatted">Hi, I am a compiler guy and not familiar with the most scientific computation. We are doing research work on R language for multi core processor. Would you like give me any suggestion...div class="preformatted">Hi, I am a compiler guy and not familiar with the most scientific computation. We are doing research work on R language for multi core pr…

updated 20.8 years ago • Cheng, Bu Qi

I am trying to import coding sequences from biomaRt using the following code (simplified example): ``` cds_seq = getSequence(id = "NM_004974", type = "refseq_mrna...I am trying to import coding sequences from biomaRt using the following code (simplified example): ``` cds_seq = getSequence(id = "NM_004974", type = "refseq_mrna", …

biomaRt

updated 2.3 years ago • andrew.b.kleist

opt)) { if (is.na(files) || is.null(files)) { stop("Error: the file name is NA or NULL.") } else { stop(paste0("Error: the file name must be a character vector. The current input is ", class(files))) } } else { if (is.na...in the file names or in the paths.")) } if…

Rsubread featurecounts coercion

updated 4.6 years ago • Konstantinos Yeles

genotype groups: wild-type (WT) and heterozygous (HET). And f<span style="line-height:1.6">or each gene per sample, I have obtained the raw read counts for two alleles (allele 1 and allele 2)</span> sample      genotype...4    HET    allele 2 count I would like to know whether the __relative abundance __of allele 1:allel…

edger allelicimbalance

updated 9.7 years ago • ugwu.nelson

I am running the presplit_map.py script on a SLURM cluster on a small dataset (MboI restriction enzyme used). here's the command I am running: ``` python presplit_map.py -G ~/../Bowtie2Index/hg19 -1 ~/../fastq/HIC003_R1.fastq.gz -2 ~/../fastq...me the following error: ``` [E::hts_open] fail to open file './tmpnA4PdG/sorted.bam' Traceback (most recent call last): File "presplit_map.py…

diffHic pysam.SamtoolsError pysam.sort

updated 6.5 years ago • shopnil99

as big as posssible) of experimentally Validated miRNAs from miRecords with their relative target genes and the 3'UTR sequences., limited to Homo sapiens. The XLS file from miRecords related the miRNA identier ("hsa-miR-xxx) with...its target genes identifier. I never found a clear way to download the miRNA sequence and the relative target 3'UTR sequence from miRecords...matched the miRNA identi…

Transcription miRNA Homo sapiens biomaRt Transcription miRNA Homo sapiens biomaRt

updated 16.3 years ago • mauede@alice.it

mauede@alice.it Cc: bioconductor List Oggetto: Re: [BioC] R: how to find the VALIDATED pair (miRNA, gene-3 'UTR-sequence) One more thing to add: >> Similarity hsa-miR-130a miRanda miRNA_target 2 120825363 120825385 >> + . 16.5359

Biophysics Biophysics

updated 16.6 years ago • mauede@alice.it

<div class="preformatted"> Hi,when I perform SAM on my array data(siggenes)I have some problems in retrieving the separate lists of up regulated and down regulated genes. When I write: fold<-function(x){ gruppi<-split(x,controllo) geni1<-abs(mean(gruppi[[2]])-mean(gruppi[[1]])) return(geni1) } fold&lt...siggenes)I have some problems in retrieving the separate list…

updated 20.3 years ago • carotenuto@igb.cnr.it

div class="preformatted">Hi, I am having problems in finding the marker names in a flowFrame. (The marker names mapped onto the channel names - i.e.FL1-H, FL2-H, FL3-H and FL4-H). I wrote the code: FCS <- read.FCS...subfilesdir2) FCS featureNames(FCS) and got this output - but it does not seem to show any new names (i.e CD45), so am I doing the right thing: flowFrame object 'P:/Pro…

updated 17.6 years ago • Anne

one slide, the result doesn't look right. What I am trying to do is: (1) export Block, Row, Column, Name, M value and weights to a text file. (2)sort the text file by Gene Name in Excel, so the same genes will appear in adjacent rows...lt;- data.frame(cbind(MA$M[,1], MA$weights[,1], MA$M[,2], MA$weights[,2], MA$M[,3], MA$weights[,3])) names(result) <- c("Rep1", "Flag1", "Rep2", "Flag2", "R…

Microarray Normalization Bayesian Microarray Normalization Bayesian

updated 21.5 years ago • Hua Weng

with non-specific probe sets). I doubt such probe sets will have much effect on GSEA results, since most of those genes will have a more specific probeset available. E.g.: > library(hgu133plus2.db) > x=as.character(hgu133plus2SYMBOL...gt; length(x) [1] 41293 #probe sets > length(unique(x)) [1] 19944 #gene symbols > ind=grep("_x", names(x)) > summary(x[ind…

Annotation hgu133plus2 probe Annotation hgu133plus2 probe

updated 12.5 years ago • Levi Waldron

Hi I'm working with non-model organism, doesn't have any information in the public domain. After denovo assembly using trinity for all 32 samples, using salmon transcript abundance level calculated and further using trinity abundance matrix scripts https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification genecount2.matrix were generated for all the datasets. My que…

tximport

updated 5.6 years ago • sunnykevin97

animal movement using different landscape patterns, and each male-female meeting get a chance of genes exchange. So, on the beginning of the simulation we define a loci structure like: LOCI_struct_start=[ [0,1,0,0,1,1] , [0,1,0,1] ] where...number of alleles (6 and 4). When female meet a male, there are a chance of female pass the genes combination to offspring, like LOCI_struct_end=[ [1,1,0,1,1,…

Genetics Genetics

updated 15.9 years ago • milton ruser

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updated 19.8 years ago • mark salsburg

Qscore/10) #Cumulated error per read. The probabilty error is increased towards the end of the sequence cum_pe <- apply(pe,1,cumsum) cum_pe[,1] [1] 5.011872e-04 8.992944e-04 1.297402e-03 1.695509e-03 2.093616e-03 2.491723e...1.258318e+02 > dim(cum_pe) [1] 300 56761 So that i have a matrix of 56761 reads of 300nt length each.</pre> How can i trim each read en…

shortread fastq

updated 10.7 years ago • danova_fr

The Problem: The SpectronauttoMSstatsPTMFormat function seems to be optimized for UniProt-style Accessions. When using TAIR10 Locus Tags, I face the following challenges: FASTA Parsing Error: When providing

Bioconductor MSstatsPTM

updated 1 day ago • srkingwu

I am using the hyperGTest function for some genesets I have and I'm having some problems with the Gene Universe & Gene set being used in the analysis. My original Gene Universe contains 18382 genes and one of my gene sets...contains 597 genes. > length(GeneUniverse) [1] 18382 > length(GeneList) [1] 597 Then I run the following to test for over-representation: > hgCut…

Annotation GO Annotation GO

updated 18.7 years ago • Vivek Kaimal

and infer gene dynamics by fitting a natural cubic splines with three degrees of freedom in order to represent the time dependence...of each gene. Could this be done at the level of 'gene programs' (aka gene signatures)? Moving what was wrote in this [GitHub issue](https://github.com...Constantin suggests three options: - The less elegant one: to modify the input matrix from genes x cell to pr…

lemur

updated 9 months ago • BiotechPedro

ala StackExchange.   Biostrings did great job for my need (align short reads to long gene) but i got Memory issue when aligning 2 big genes using global alignement.  There is also similar post regarding Memory...match=1, mismatch=0, baseOnly=TRUE) seqlns=seq(100, nchar(refS), 10000) runT=rep(0,length(seqlns)); names(runT)= seqlns    &…

Biostrings pairwiseAlignment

updated 11.2 years ago • branislav misovic

and 1 technical covariate, however, so should `K` be set to reflect this? - **Should I filter genes for the dimensionality reduction step?** - I have tested the top 1000 most variable genes and the entire set of 16000. If I...dispests_ulinput][3] My interpretation of this plot is that the dispersion of lower count genes (<1000 counts) is large; large enough to weaken my ability t…

DESeq2 ZINB zinbwave deseq

updated 4.9 years ago • rowcyclecamp

I load the library, read a genome sequence into memory (it's tiny), and create DNAString objects out of a column of short sequences stored in my data frame `data...Biostrings) genome=readDNAStringSet("O_sativa_japonica_Oct_2011.fa") query_seqs = sapply(data$Sequence,DNAString) ``` A bit more info: The object `data` is a data frame with one column (`Sequence`) that contains short oligonucleotide…

IRanges MIndex

updated 4.5 years ago • Ann Loraine

unlist(chr), ll, unique) Error in tapply(unlist(chr), ll, unique) : arguments must have same length >length(chr) [1] 2400 >length(ll) [1] 2400 >length(unlist(chr)) [1] 2408 > Is this caused by a bug in "unlist" like an unaccessable

updated 21.5 years ago • Irene Li

the reasoning seems logical. > We recommend that reads or fragments overlapping more than one gene > are not counted for RNA-seq experiments because any single fragment > must originate from only one of the target...genes but the identity of > the true target gene cannot be confidently determined. On the other > hand, we recommend that multi...overlap reads or …

RNA-Seq featureCounts Rsubread

updated 11 months ago • Arindam

new to bioinformtics and Bioconductor. Why does GOstats resp. the GO annotation package use entrez gene ids? I thought, that GO terms are associated with proteins. And cause one gene can be translated to diffenent proteins, analyzation...only with gene ids will perhaps be problematic. Especially if the data consists of miRNAs or Proteins and you have to convert it back...to gene ids. So why does …

Annotation GO GOstats Annotation GO GOstats

updated 18.9 years ago • Kai Schlamp

I would like to do a per gene ancestry covariate.  I believe this could be important because ancestry for portions of chromosome can be different...in the same individual so there is no way to correct across all genes with a simple covariate.   Is there any way to do this with DESeq2?  I am already using CQN to do gene length and GC

deseq2 ancestry

updated 9.0 years ago • kodream

from Chr19. I am using the following: txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene genes_txdb <- genes(txdb) however, the genes are listed by id. I want to add the gene names to my GRanges object. Is there a way to map the gene id...to the gene name? Thank you

GRangesobjectmodification

updated 3.0 years ago • Gamal

human_ensembl, pattern = "start_position") name description page 10 start_position Gene start (bp) feature_page 210 start_position Gene start (bp) structure 250 start_position...Gene start (bp) sequences # generate all possible attributes with pattern "hgnc_symbol" biomaRt::searchAttributes(human_ensembl...pattern = "hgnc_symbol") name descri…

biomaRt cdna keys gene_start

updated 5.0 years ago • bastien_chassagnol

Hi Weijun, In terms of the topmost metabolic pathway "hsa01100", I would like to highlight some enzymes on this pathway, however, it seems the "circles" on the plot are metabolites instead of enzymes. The enzymes are the "edges

updated 12.5 years ago • Ed

below. I looked at 3 of the discrepant SNPs using the UCSC genome browser (to visually confirm which gene was infact closer). It seemed to me that one version mapped the SNP to the nearest gene and the other seemed to somehow be...strand aware (ie it mapped it to another gene that was in the vicinity but happened to be oriented opposite to the true nearest gene). EDIT: --- An example.…

GenomicRanges distancetonearest strandedness

updated 7.8 years ago • shraddha.pai

p values and logFC values and another one that uses the MarrayLM object as input and labels the top gene hits. Here are the source links: 1)  http://www.gettinggeneticsdone.com/2014/05/r-volcano-plots-to-visualize-rnaseq...html/volcanoplot.html (can only be used for Limma I believe) Is there a way I can label the top 20 most up-regulated genes and 20 most down-regulated genes…

volcanoplot

updated 8.2 years ago • Nithisha