Bioconductor Forum

before? How could I solved this problem? Thanks! My workflow were as following ## import the genes ID which I fetch from Ensembl HZ254gene_data <- read.delim("E:/HZ_GO_enrichment/HZ254gene_data.txt", quote="") colnames...HZ254gene_data)[1]="locus_tag" ## get assayed gene vector assayed.genes=HZ254gene_data$locus_tag assayed.genes1=as.vector(assayed.genes) is.vector(assayed.gen…

RNASeq GO goseq DESeq2 RNASeq GO goseq DESeq2

updated 11.9 years ago • 刘鹏飞

Dear all, please may i ask a simple question : in BioC, what is the simplest (or the most direct way) to retrieve **the COORDINATES of EXONS for RefSeq or ENSEMBL genes** ? thanks a lot, -- bogdan

txdb genome exons

updated 6.4 years ago • Bogdan

div class="preformatted">how to combine transcripts of one gene i have a fasta file which have many transcripts i want to cluster those transcripts to the gene level without the reference...genome sequence which package can do so? thx -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road

updated 13.9 years ago • wang peter

I want to create a plot to show how desired genes are located across the different chromosomes with IdeoViz. How can I create a GRanges object that includes 24 chromosomes...but only genes that I want? The plot needs it as input

GRanges gene symbol IdeoViz

updated 7.1 years ago • Arman Shahrisa

to quality control of count data, and the results recommended normalization for GC content and length. But I have studied some papers and have founded that GC content and length normalization in gene expression comparison

normalization

updated 7.9 years ago • parvin.shariaty

Hi All, I will like your advice in how to present the DE genes in a heatmap. I will like to show around 40 genes of interest, their log2FC varies between -1.3 to 5.4, but most of them...range between -1 to 1. One gene can be DE (FDR<0.05) in one but not all the datasets and I want to show this in the heatmap. But not sure how to deal with them

deseq2 heatmap

updated 11.0 years ago • Catalina Aguilar Hurtado

modules_names, col = module2colors_colors) ) cell_type_legend <- Legend( labels = names(celltype2colors), # Cell type names legend_gp = gpar(fill = celltype2colors), # Corresponding colors title = "Cell Type" ) cell_subtype_legend...lt;- Legend( labels = names(cellsubtype2colors), # Cell subtype names legend_gp = gpar(fill = cellsubtype2colors), # Corresponding c…

ComplexHeatmap

updated 14 months ago • nromerov

sample3 - ALL sample4 - ALL sample5 ---------- I am finding differentially expressed genes in sample(n=5) and control(n=3) data using stattest() function in R to get most variance. But I am unable to load both sample and...and control in separate ballgown objects? But if so how can I calculate differentially expressed genes between the groups? If I need to process together I might h…

ballgown i_data.ctab differential gene expression

updated 5.3 years ago • pushgct

there exists in Bioconductor something like the matlab command "getgenbank". It serves to retrieve sequence information from the GenBank database in a simple way, and to download just the sequences to analyze them. I have seen...the GEOquery and seqinr libraries but I could not download some given mitochondrial sequences. Best jm~ _______________________________ J. Miguel Marin http:…

GEOquery GEOquery

updated 17.5 years ago • JUAN MIGUEL MARIN DIAZARAQUE

Then i did log-fold shrinkage using the apeglm package and im getting differentialy-expressed genes with significant p-values but very small logfold changes, for example 0.0006, which should be the result of many samples...i think. When i make a volcano plot i see genes overlapping at the center of it, something that does not happen when differential expression without log-fold shrinkage…

deseq2

updated 7.1 years ago • sherajilir

div class="preformatted">hi netters, i have a gene expression matrix where rows are genes and columns are conditions. The values are either "A"(absent) or "P"(present). There are...15 conditions in total. If a gene is absent in most of these conditions, say at least 13 out of the 15 values are "A", then I would like to remove this gene from...the matrix. So finally I'll get a new matrix with …

updated 20.7 years ago • zhihua li

i have a data set of 91 uniprot id's across three time points.I wish to perform differential gene expression analysis using edgeR. I checked&nbsp

differential gene expression edger

updated 7.5 years ago • prakashpandey1111

samples, you can expect a lot of very high correlations just by chance. So, you should filter your genes by some criterion of "interestingness" before performing correlation analysis. --Naomi At 12:02 PM 6/28/2010, Steve Lianoglou...for each sample. > > > > I want to look at the expression correlations between genes. Say, my gene > > of interest is gen…

Cancer affy Cancer affy

updated 15.5 years ago • Naomi Altman

Dear Dr. Smyth, We are analyzing some RNA-seq samples collected in different batches, where the batch is a known variable. To account for that we reasoned we could use a linear model to include the batch effect and then remove it.  Since the voom+limma approach is shown to work well for differential gene expression, we thought of estimating the weights for each observation through voom…

voom limma clustering removebatcheffect() batch effect

updated 10.5 years ago • ale.breschi

14 10:56 AM, "Shamit Soneji" <shamit.soneji at="" med.lu.se=""> wrote: > Hi Julie, > > My name is Shamit, I'm a bioinformatican at Lund University Sweden who > has been asked by a colleague to find CRISPR sites for...lt;- readDNAStringSet(inputFilePath, format > > > for(i in 1:length(subjects){ > #does stuff here > } > &…

updated 11.5 years ago • Julie Zhu

Dear reader I am using edgeR to do differential gene expression analysis on my mRNA seq data. I have a question about what would be the proper way to do my differential gene...to do any other comparisons). But the data was acquired in one experiment and also the samples were sequenced together and are part of the same story let's say. Basically, the same situation as above, only here the co…

edgeR

updated 24 months ago • Jurgen

with the > way the HTSeq python scripts deal with the exons that overlap with more > than one gene ID. > > The solution that we had taken so far was that the gene IDs sharing an > exon were merged into an "aggregate gene...ID. From the input of some > users and our own experience, we know that it was not the most > appropriate solution: when the m…

DEXSeq DEXSeq

updated 11.8 years ago • Rao,Xiayu

preformatted">Is there an elegant way to find the chromosome, start and end position to a given gene symbol via rtracklayer. In the table browser on USCS website I can provide these information by pasting a list of identifiers...somewhere in the tables. My found solution is kind of indirect by first getting a table of all UCSC names together with gene symbols, finding the corresponding UCSC …

rtracklayer rtracklayer

updated 16.5 years ago • Christian Ruckert

Hi, I'm trying to match a `` vector `` of peptide sequences against an `` AAStringSet `` to get all perfect matches. I thought the most straightforward way to do this is to create...Hi, I'm trying to match a `` vector `` of peptide sequences against an `` AAStringSet `` to get all perfect matches. I thought the most straightforward way to do this is to create a `` PDict `` object from the&…

biostrings pdict

updated 8.9 years ago • rubi

div class="preformatted">Hi, I've posted the same question to the bio-sig-sequencing list ( https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2010-September/001564.html) two days ago, but also interested...GCG') z <- DNAStringSet('AGA') foo <- rep(list(x,y,z),1) # I was exploring to see if the length of the list made a difference (it doesn't) do.call(c, foo) # creates a DNAStr…

updated 15.3 years ago • Andrew Yee

I get this error: ```r > atrack <- AnnotationTrack(gene, name = "Gene Model") # Error in (function (classes, fdef, mtable) : unable to find an inherited method for function '.buildRange' for

annotationTools

updated 3.2 years ago • jt.cathey

Hello everyone, I compared 2 examples to find a list of common genes. Once I have found the common genes, I would like to find out the main processes to which these genes belong. I have an excel...or CSV file with a table with a list of genes, the name of each gene and its GOs number. I do not have statistical information on each gene, how can I find the main processes...none of the options so …

GeneSetEnrichment genes genetogo

updated 3.6 years ago • Noy

Hi, I want to use DESeq2 for assessing allele-specific expression. I will compare gene-level allelic counts of a yeast hybrid (basically comparing counts of orthologous genes of parentals of this hybrid..._e9d578fe1f7a404aad0553f52236c0a4.html. My question is that parentals might have orthologous genes with different lengths, so for example ortholog in parent A is 1000bp and in parent B …

deseq2 allele-specific-expression rnaseq

updated 7.7 years ago • gtechbio

I used AnnotationForge to build an annotation package. And when I use `` makeDBPackage `` function, it does not work as printing "Error: Parameter 0 does not have length 1." <pre> Error: Parameter 0 does not have length 1. 12 stop(structure(list(message = "Parameter 0 does not have length 1.", call = NULL, cppstack = NULL), .Names = c("message", "call", "cppstack"), class = c("R…

AnnotationForge

updated 10.0 years ago • zhilongjia

using WGCNA for constructing Coexpression Networks . I am now at the point where I am prioritizing genes for candidate hubs. I saw that there are different methods for choosing hub genes in a module. I saw that some people have...reported using the 0.8 cutoff for MM ( correlation of the gene with the Module Eigen of the module). But I can't get any hubs for most module that can reach to 0.8. The …

wgcna WGCNA hubgenes

updated 4.8 years ago • Hanna

DESeq2. After running ```dds<- DESeq(dds)``` i wanted to retrive all the up and down regulated genes. i gave the conditionpvalue < 0.05 and log2FoldChnage > 1.5 for up regulated genes. But in the result file also include...the genes which have pvalue > 0.05. iam pasting my example dataset here with the result. I wnted to know that which command will...be helpfull here…

Bioconductor Transcriptomics DifferentialExpression DESeq2

updated 2.6 years ago • sreeshmaraj72

with a NGS protocol in which we insert sheared genomic fragments into a custom plasmid for sequencing on an Illumina MiSeq instrument. The insertion site of this plasmid is flanked by our own custom barcodes (N7) and...80 nt Illumina-based adaptor sequence. We then PCR out the insert with barcodes and adaptors for sequencing. Our adaptor sequence is similar to the Illumina...long enough that we h…

Sequencing Cancer Biostrings Sequencing Cancer Biostrings

updated 12.5 years ago • Taylor, Sean D

Hi Given a _GRangesList_ object `` grl ``, running <pre> lapply( grl, length )</pre> is very slow. Why is that? What should I do instead?   Background and example: I want to get, for all human genes, the...gt; transcripts <- transcriptsBy( TxDb.Hsapiens.UCSC.hg19.knownGene ) > genes <- reduce( transcripts ) </pre> I was happy to notice that…

GenomicRanges GRangesList

updated 10.0 years ago • Simon Anders

algorithm assumes a linear model with an intercept and I would rather use one without it as it is most natural in order to simply compare two groups. Thanks, augusto </div

GO limma sva GO limma sva

updated 17.5 years ago • Augusto Rendon

Hi there, Michael, First, thanks for the great software and the excellent documentation you all have provided. My question is more theory-based. I'm interested in characterizing a mixed community as a whole. I've co-assembled metatranscriptomes, called genes, and used these coding sequences as my reference library during mapping of individual samples to create my count matrix - which i then norm…

deseq2

updated 9.0 years ago • AstrobioMike

I am trying to retrieve flanking sequences of target genes in *Chlamydomonas reinhardtii* from **Phytozome** with `getBM()`. I was able to load the Phytozome database...I am trying to retrieve flanking sequences of target genes in *Chlamydomonas reinhardtii* from **Phytozome** with `getBM()`. I was able to load the Phytozome database successfully with `useMart`: mart=useMart(biomart = '…

biomaRt getBM Phytozome Chlamydomonas

updated 5.8 years ago • ytlin610

Hello Bioconductor community, I have used DESeq2 to test for differences in the overall transcriptional activity of species in a microbiome sample. However, i am not quite sure whether what I'm doing is correct. Thus, I would be very thankful for somebody confirming that this solution makes sense or pointing me to an error. I am comparing two different biological conditions. For each condition,…

Metagenomics DESeq2 Metatranscriptomics

updated 4.7 years ago • Tom

research interest, the data I am planning to work on is qPCR data, with much smaller number of genes (from around 30 genes), with relatively big sample size (1000 samples, highly heterogeneous). Apparently I could not...scale free topology, and identifying any big module, which I think is because of the small number of genes. I looked up a lot but could not find anyone asking ab…

WGCNA

updated 8.9 years ago • zson3366

div class="preformatted">Hello, I have a list of genes which are not official gene symbols. Normally in this case I would search gene in entrez to see if it is an alias and then

Cancer Cancer

updated 16.8 years ago • Daniel Brewer

Hello! We are looking at extra cellular RNA which has been collected from cell culture media. We used UMIs to tag and sequence nucleotides which were present in the media, processed them with nf-core RNA-seq pipeline and generated counts using subreads. Due to the nature of data, we are not sure if we can expect any consistent expression across/within sample groups. For now we have just follow…

RNASeq DESeq2

updated 2.2 years ago • Karthik

in the field of translational research (e.g. Kraiczy et al. Mucosal Immunology 2016, Cannavò E et al Nature 2017, Baud A et al, PLoS genetics 2017, McKinney EF et al Nature 2015) and apply cutting edge computational biology approaches...statistics/probability and machine learning are essential. Previous experience in RNA and DNA sequencing, gene regulation and expression analysis, and/or modelin…

postdoc bioinformatician biomedical informatics bioinformatician job job Job

updated 8.9 years ago • kraiczy

Since looking at the row variance and DESeq2 both act as ranking mechanisms for genes, is there any sense to taking the top 1000 or 5000 genes with the highest variance across samples from an RNA sequenced...set and running the DESeq2 pipeline on that subset to look for differential genes between groups (so simple design ~condition)? Thanks!&nbsp

deseq2 variance genes

updated 8.1 years ago • hs.lansdell

I generated the matrix using the tximport package. I have transcript ids as my rows and the sample names are the columns. <pre> txi <- tximport(files, type="salmon", tx2gene=NULL, ignoreTxVersion=TRUE,dropInfReps=TRUE,txOut = TRUE...tpm <- (txi$abundance[apply(txi$abundance, MARGIN = 1, FUN = function(x) sd(x) != 0),]) tpm = log2(tpm + 1) tpm_centered <- t(tpm-row…

pca tpm tximport

updated 8.2 years ago • tanyabioinfo

Hi, I am working with snRNA-seq data and performing pseudo-bulk differential gene expression analysis using DESeq2. To do this, I did pseudo-bulk (aggregate counts across the cells). Then, I selected a specific...fewer neurons compared to controls. My question is: Does performing pseudo-bulk and differential gene expression of specific cell types account for differences in cell type abundance…

SingleCellData DESeq2 pseudobulk sing

updated 10 months ago • Sara

3 biological replicates = 3 independant inoculations). One sample is problematic as out of 44,480 genes, 780 are highly expressed in that same sample but are at 0 for the 5 other samples. Using sample to sample distance, this...sample clusters alone and the levels of expression of these genes are very high (almost 1,200 reads for one of these genes). But aside this rather small amount of genes,…

RNAseq DESeq2 outlier counts DE analysis

updated 5.6 years ago • DcL-A

gt; Dear Bioconductor community, > > > > I've been looking for differentially expressed genes in C. elegans after a > > drug treatment. > > There are 3 replicates of each condition and 2 conditions in total (WT and...very poor > > overlap in the results: > > > > - example (i) only 24 of the 100 most …

Normalization limma Normalization limma

updated 20.4 years ago • Naomi Altman

Hi, I was trying to do some comparative analysis between the rhesus and human genes. I seem to get no genes that are common to both species! What am I doing wrong? My code, screen output :   ============= library("TxDb.Hsapiens.UCSC.hg38.knownGene...txdb\_rh8 <- TxDb.Mmulatta.UCSC.rheMac8.refGene \#\# All rhesus entrez ids grgenes <- genes(txdb\_rh8) allrefs &l…

org.hs.eg.db org.mmu.eg.db

updated 7.7 years ago • Brian Smith

I am analyzing some Illumina BeadArrays downloaded from GEO, but when annotating the results I noticed the `` select `` function can apparently not access all annotation information. I think this is a bug, but please correct me if this is intentional... The arrays are Sentrix Mouse-6 v1.1 arrays, and I use the `` illuminaMousev1p1 `` [package](http://bioconductor.org/packages/release/data/annota…

annotation annotationdata illuminaMousev1p1.db

updated 9.0 years ago • Guido Hooiveld

Dear BioConductors, I'm looking for a way to "cut" out a "slice" of aligned sequences from a BAM file given start and end positions in the reference sequence. I have looked at the GenomicAlignments...construct a ScanBamParam call that picks out the reads overlapping my region of interest, but the sequence I get out in the $seq metadata column is the full sequence of the read - not only the sequ…

bam granges genomicalignments

updated 10.5 years ago • Thomas Poulsen

dev <- computeDeviations(object = rse, annotations = motif_mm) ``` ``` Error in names(res) <- nms : 'names' attribute [386] must be the same length as the vector [302] In addition: Warning message: stop worker failed...dim: 4446140 386 metadata(0): assays(1): motifMatches rownames: NULL rowData names(2): name bias colnames(386): MA0025.1_NFIL3 MA0030.1_FOXF2 ... MA090…

chromVAR computeDeviations

updated 5.5 years ago • mkarimzadeh

DESeq2) library(microbiome) library(ggplot2) data("dietswap") a <- rowMeans(abundances(dietswap)) dfs <- data.frame(taxa = names(a), mean_abundance = a) %>% arrange(mean_abundance) %>% mutate(taxa = factor(taxa...stat = "identity") + labs(x = "taxa", y = "Mean read count (N)", title = "abundance curve") print(p

deseq2

updated 5.8 years ago • wisam.tariqsaleem

now and I keep getting one cluster. I was wondering if there may be something wrong with the abundance txt file i'm feeding into the package? The Format of my abundance txt file is as follows: Column 1: A list of all the Taxa...Row 1:  A list of all the sample names Any help/advice would be greatly appreciated.   Thank you all Dr. Imran Sulaiman

dirichletmultinomial dmm

updated 8.7 years ago • amgodogma

Hi, after an RNASeq analysis using Limma I obtained a table full of genes by using the topTable() function. So I have a csv, comma separated, formed by GENEID(ensemble), ENTREZID, SYMBOL, logFC, AveExpr...t, P.Value, adj.P.Val, z.std. Is there a way to search the most significant genes associated to a specific disease mentioned in some papers? Because for e.g. the top 5 genes are not mentioned…

GeneExpression RNASeqR limma

updated 5.1 years ago • Will

Hi, I have a set of sequences blasted against NCBI RefSeq and I want to retrieve the GO-terms for the gene names, similar to what Blast2GO does

GO BLAST annotation

updated 11.2 years ago • Jon Bråte

Hi everyone, I am trying to use TxDb.Hsapiens.UCSC.hg19.knownGene to get the nearest genes. I tried to put in the range for PLCXD1 (chrX:198,061-220,022) but interestingly the nearest gene found is LINC00102...pre> library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) library(ChIPpeakAnno) genes <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene) genes[neares…

txdb.hsapiens.ucsc.hg19.knowngene ChIPpeakAnno

updated 9.6 years ago • C T

Hi - I'd like to apply CopywriteR to detect CNAs in my targeted Capture sequencing data based on a gene panel of  about 150 kb - in the documentation, it is suggested to start with a bin size of 50

copywriter bin size targeted sequencing

updated 9.9 years ago • sshung

I am wanting to delete about 9000 rows of genes from 27,000. The rationale is that 20 of our samples are "identical" in the sense that they have all been deleted for an essential...gene (permitted due to a drug pretreatment),(aka biological replicates), and the 9000 genes show very strong variation between...things like %in% and intersect, but no luck (I am guessing because the rows are differe…

deseq2

updated 6.4 years ago • rattray56

<div class="preformatted">Hi, after going over the user guide and searching this mailing list I'm not quite clear on how to best address my specific situation: I'd like to test differential "expression" of specific splicing events between a mutant and the wild type in a replicated design. To do so, I've specifically counted reads that are specific to a certain splicing event for each gene…

edgeR edgeR

updated 11.7 years ago • Guest User

div class="preformatted">Hello List, sorry if this is a stupid question, but I am returning some old sequences that I have laying around, the program is a mac program called MacClade, but the sequence file looks like: #NEXUS [MacClade...Did I overlook some function in the "seqinr" package? Before I write some function to get the sequences out for me. Thanks for the help! Cheers, Brian </…

updated 13.9 years ago • Brian

<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-Feb-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 13.0 years ago • Martin Morgan

<div class="preformatted">Bioconductors! There are still spaces in our forthcoming 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...still spaces in our forthcoming intermediate course on use of R / Bioconductor for high-throughput seque…

Cancer Cancer

updated 12.7 years ago • Martin Morgan

Hi,         I'm doing RNA-Seq data analysis following nature protocol paper (Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown...Hi,         I'm doing RNA-Seq data analysis following nature protocol paper (Transcript-level expression analysis of RNA-seq experiments with HISAT, St…

genefilter ballgown

updated 8.0 years ago • fubeide

filters based on intensity values and then pulls >sequence data for the probes which satisfy the >intensity based filter. I notice that results given by >the script are...from the sequence data files >which Affymetrix supplies! > >Here are top three seq. from my result and below these >are the sequences...for the same probe ID's from >Affyme…

GO cdf probe GO cdf probe

updated 20.9 years ago • Justin Borevitz

Hi, I am trying to find out length of Yeast ORF. Where is my mistake? <pre> > sacCer3Length <- function(symbols) { require(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene...require(org.Sc.sgd.db) exons.db = exonsBy(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, by='gene') egs = unlist( mget(symbols[ symbols %in% keys(org.Sc.sgd) ],org.Sc.sgd) ) sapply(egs,function(eg)…

yeast genomicranges

updated 11.2 years ago • dktarathym

enter image description here][1] I generated a custom annotation using IsoQuant and long-read sequencing data. I did not find any missing gene names or placeholders within the custom annotation. This is from a 2X2 RNA-sequencing...experiment looking at gene expression in the deer mouse placenta. featureCounts -O -M --fraction -p -F GTF -t transcript -T 24 -a OUT.extended_annotation.gtf

featureCounts Rsubread

updated 7 months ago • Meg