Bioconductor Forum

div class="preformatted">Hi all, We present a new R package DEGseq for identifying differentially expressed genes from RNA-seq data.The input of DEGseq is uniquely mapped reads from RNA-seq...Comments, questions, etc, are all welcome. Best regards Likun [[alternative HTML version deleted]] </div

Annotation DEGseq Annotation DEGseq

updated 16.1 years ago • Likun Wang

Hi group, I am interested in retrieving about 2000 sequences with the specific chromosome number,start and end site. I was thinking of using BSgenome package for this. >source("http://bioconductor.org/biocLite.R...would work for specific values. #So I tried to use a dataframe where it would retrieve chromosome number from by using >full<-as.matrix(read.table(test_seq.txt…

BSgenome BSgenome BSgenome BSgenome

updated 14.3 years ago • viritha kaza

are the ones that show decrease in BMI from T1 to T2. I want to use continuous variable (BMI) to identify genes that are predictors of response to diet. I also have other co-variates that need to be controlled like age &amp...reduced=~Gender+AGE) res=results(dds, contrast=list("T1.BMI","T2.BMI")) ``` Is this right to identify the genes that could be potential identifiers of responders to t…

DESeq2 rnaseqGene DifferentialExpression

updated 22 months ago • Abhishek Singh

Dear All I am trying to find differential use of exons across entire genome for two conditions, total number of samples are about 88 (which is a lot for DEXSeq, I am aware of that), I've been trying newest version of DEXSeq\_1.26.0 with 50 cores and 1000GB of shared memory, however with days of running I still couldn't get through the estimateDispersions step. Now I am thinking if I ca…

dexseq

updated 7.2 years ago • slowsmile820

9 } 10 } What is the difference between line 3 and line5? In the line 3 I retrieved the GO identifiers at level 2 successfullly but in the line 5 I got nothing. How to correct the line 5 to retrieve the GO terms at level

GO PROcess GO PROcess

updated 21.2 years ago • szhan@uoguelph.ca

<div class="preformatted">Dear Gowthaman, There's no rigorous answer to this question, because it depends on the variability of your population, how large the fold changes are that you want to detect, how many genes you need to find, what FDR you can tolerate, etc etc, and it's impossible to know all these things in advance. However, we can learn from experience. At our institute, we reg…

RNASeq Organism edgeR RNASeq Organism edgeR

updated 13.5 years ago • Gordon Smyth

<div class="preformatted">I'd like to take advantange of the segmentation algorightms in cn.mops, to estimate copy number from low-coverage BAM files. The average coverage in our tumor and normal DNA, is about 0.8 and 0.7 respectively, quite uniformly across the whole genome. The consistency of the reads, and their ratios, allow us to plausibly identify amplifications and deletions, eith…

Sequencing Coverage cn.mops Sequencing Coverage cn.mops

updated 12.6 years ago • Paul Shannon

value<=0.05 and |FC|>2 as the criteria to screen differentially expressed genes. If I want to identify genes with similar expression under different conditions, which criteria should I use? I was thinking of only using

deseq2

updated 5.8 years ago • wangy660

find a reply and I have the same question. I was looking for a package that provides functions to identify minimum common genomic regions of interests based on segmented copy number data from multiple samples. I've found...using other method. This segment list has the same parameters: 1)the sample id, 2)the chromosome number, 3)the map position of the start of the segment, 4)the map position of t…

DNAcopy cghMCR DNAcopy cghMCR

updated 14.2 years ago • viritha kaza

I would like to get the number of cases added (created, any logical datetime would suffice here) to the TCGA project by experiment type. I attempted...to get this data via `GenomicDataCommons` package, but it is giving me I believe the number of files for a given experiment type rather than number cases. How can I get the number of cases? Here's my attempt: First...17:01.373309-05:00 …

TCGA GenomicDataCommons

updated 4.7 years ago • Ezgi

i need scientific paper to know how to identify the sequences bio-markers for specific disease, and how to use it to detect the existence of the disease...!!&nbsp

dnaseq pathway analysis protein biomarkers

updated 7.8 years ago • emadelhewihy

div class="preformatted"> Hi, I have a question regarding the minimal number of genes that we can test in an analysis with edgeR. Let me explain, in a study, edgeR have been used for testing the differential...as there is two replicates per condition). The library sizes, however, correspond to the total number of tags aligned both on these viruses and on the genes of the host organism. It se…

Organism edgeR Organism edgeR

updated 13.1 years ago • Guest User

Hi, I use the DSS package to identify DMRs. I has already written a script that worked very well with the first data that I had tested. I wanted to reuse this...someone give me some leads to test ? Thanks in advance, Bernadette ``` SessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default …

software error

updated 5.4 years ago • bernadetterubio

effect should prevent any great problems. My main questions are; 1. I would like to identify which transcripts appear to be specific to an individual tissue from my 8 2. Which genes are ubiquitously expressed...across all 8 Cheers Dennis [[alternative HTML version deleted]] </div

edgeR edgeR

updated 14.5 years ago • Dennis Gascoigne

Hi, I have used Deseq2 packages for months but today when I tried to install the package, using BiocManager::install("DESeqDataSet") I received: Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05) Installing package(s) 'DESeqDataSet' Update old packages: 'sys' Update all/some...install the package, using BiocManager::install("DESeqDataSet") I …

deseq2

updated 6.3 years ago • HAILYTR

to look at genes that are constituently expressed across samples, but not differential. So far, I identified genes with a p-value of >0.05 (I understand this comes with the caveat of that gene simply having no evidence for...TPM >= 3. I was wondering if this approach seems reasonable, or if there is a better method for identifying constituently expressed genes? Thank you so much …

DESeq2

updated 3.1 years ago • nute11a

ComplexHeatmap` or `coolmap`). Here, unsupervised refers to employing a list of genes that is not identified through group comparisons (i.e. not informed by grouping labels). Typically, such lists would be filtered based...do this. Please provide suggestions if there is a built in method in `EdgeR` or a efficient way to identify identify top most variable genes. Thank you, Mohammed

supervised edgeR variance RNASeq heatmaps

updated 2.9 years ago • mohammedtoufiq91

nbsp;How many sequences do you recommend using to identify the off-targets with the Guide-Seq method? Best regards Jacques P. Tremblay   Answer from Dr Zhu: It depends on how...many offTargets you expect and whether you are interested in identifying low incidence of offTargets. We often sequence half to one million reads per sample

sequencing

updated 7.6 years ago • Jacques-P.Tremblay

for annotation. I am trying to build the gene length database by myself, given that the current version of goseq does not support the mm10 build. 1, Cufflinks seems ignored the original gene identifier that comes with the...and make its own, but they do keep the gene name in its record, so I will just take gene name as identifier in my process. I have already used the gene names for building th…

Annotation GO PROcess goseq Annotation GO PROcess goseq

updated 12.5 years ago • Xulong Wang

Hi, I'm very new in the field and would appreciate any help. I want to identify if a certain protein is differentially expressed between two sets of population from the TCGA database. Before

DifferentialExpression TCGAWorkflow

updated 4.1 years ago • Se Jin

human.  The background size is 16309. Panther webtool give a size of 21002. __Annotation Version and Release Date:__ GO Ontology database Released 2017-08-14 I was wondering which version of the GO database...is use in ClusterProfiler. Why these numbers are differents ? I'm using something like. <pre> edb = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_g…

clusterProfiler

updated 8.2 years ago • ZheFrench

<div class="preformatted">I just tried to send this mail to the list but it seems as if it didn't go through - I will make another try. ______________________________________________________________________ ___ Dear list, This might be a question that has been discussed previously but I could not find any good solution for it. I have lists of human proteins from various proteomics studies…

Proteomics Coverage GO Proteomics Coverage GO

updated 18.5 years ago • Lina Hultin-Rosenberg

When testing more gene sets with `` mroast ``, should number of rotations be increased to maintain the accuracy of p values? If I use x number of rotations for testing 1 gene set, should...When testing more gene sets with `` mroast ``, should number of rotations be increased to maintain the accuracy of p values? If I use x number of rotations for testing 1 gene set, should I use perhaps 10x numbe…

limma mroast

updated 7.3 years ago • siajunren

makeTxDbFromBiomart also by reproducing the function help examples. Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line 7 and body...4 and html Premature end of data in tag html line 2 Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYST…

software error maketxdbfrombiomart

updated 10.0 years ago • luigi.cerulo

I am getting this error when trying to biocLite() the latest version:   <pre> Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/****/R/x86_64-pc-linux-gnu-library/3.4...I am getting this error when trying to biocLite() the latest version:   <pre> Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared …

ChAMP

updated 7.7 years ago • yura.grabovska

Hi, I hope someone can help with this.   You will see by my lack of providing the appropriate information necessary for you to actually diagnose this (ie, error logs) that I am an R noob.  Please point me to the correct logs and I will happily provide them! The edgeR function processAmplicons is causing R (rstudio <span style="background-color:rgb(243, 244, 244)">Version…

edger processamplicons rstudio

updated 10.5 years ago • thomas.leete

However by using the web service www.biomart.org I received ~48000 transcripts for the same genome version and chromosomes. By comparing these two data frames you could see that the discrepancies in number of transcripts...only for some chromosomes (3:9 and X). If I specified only two chromosome names (2 and 3) than the number of downloaded transcripts is correct for both of them. If I did not s…

Annotation biomaRt Annotation biomaRt

updated 16.1 years ago • Ivanek, Robert

states. I already identified a set of signatures (set of transcript cluster id lists) but, for some of these signatures the number of features...HuGene-1_0-st-v1.na30.hg19.transcript.csv) from Affymetrix and extracted some informations: Total number of transcript cluster id: 33257 (29096 when controls are removed) Number of transcript cluster ids with an assigned...gene: 22118 Number of different…

Annotation Annotation

updated 15.9 years ago • Nizar Touleimat

advantages over existing methods, including the use of either continuous of user-discretized copy number data. Also, our model allows for using confounder variables, such as clinical variables, and does not require mapping...between copy number and expression probes. The package includes many tools for visualization. A limited number of those is already available...on the current devel version, w…

SNP Microarray Visualization Cancer SNP Microarray Visualization Cancer

updated 17.2 years ago • Maarten van Iterson

Hi Love, I am using DESeq2 for identifying DEG through RNASeq data. In this step, dds <- DESeq(dds) res <- results(dds, name = "SampleGroup_Tumor_vs_Normal...Hi Love, I am using DESeq2 for identifying DEG through RNASeq data. In this step, dds <- DESeq(dds) res <- results(dds, name = "SampleGroup_Tumor_vs_Normal") For

DESeq2

updated 4.4 years ago • Akhilesh

script again with same parameters and same input, but I got different result, e.g. I found a higher number of upregulated genes compared to the run two weeks ago. When I check for given genes in my old and new results I can see...below 1 in my two week-old results, but now its in above 1 in most cases. I saw that a new version of DESeq2 was released some days ago. Now my question: Was…

deseq2

updated 7.3 years ago • hinkel2

<div class="preformatted">miRecords VALIDATED miRNAs have a (I guess) unique Mature Accession Number (MIMAxxxxxxx) associated with them. in the he FASTA file from: "ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/mature.fa.gz...div class="preformatted">miRecords VALIDATED miRNAs have a (I guess) unique Mature Accession Number (MIMAxxxxxxx) associated with them. in the he FASTA…

updated 16.4 years ago • mauede@alice.it

GAGE12F, GAGE12J, GAGE12D, GAGE5, GAGE6, GAGE12B, GAGE4, **GAGE12G, GAGE12I, GAGE7 (GAGE2E was not identified)**. And I cannot use select() from AnnotationDbi, because my data has an AffyHTAPDInfo signature, not ChipDb. How can

clariomdhumantranscriptcluster.db MicroarrayData Microarray pd.clariom.d.human

updated 3.6 years ago • amir.rakhimov.b

Hi, I am working with RNA-Seq Illumina PE – 150 bp dataset. I was wondering if there is a way to identify contaminations (such as mitochondrial DNA contamination, any other types of contamination) in the data, and remove

rsem STAR Alignment quantification Bowtie

updated 2.9 years ago • Abdul

<div class="preformatted">miRecords VALIDATED miRNAs have a (I guess) unique Mature Accession Number (MIMAxxxxxxx) associated with them. in the he FASTA file from miRBase: "ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT...div class="preformatted">miRecords VALIDATED miRNAs have a (I guess) unique Mature Accession Number (MIMAxxxxxxx) associated with them. in the he FASTA file…

updated 16.4 years ago • mauede@alice.it

Error in DGEList(counts = D, group = c(rep("d45HVC", 2), "d45WB")) : Length of 'group' must equal number of columns in 'counts' So there is no way for me to use all my information (columns) ? Lana Schaffer Biostatistics, Informatics...DNA Array Core Facility 858-784-2263 [[alternative HTML version deleted]] </div

updated 14.5 years ago • Lana Schaffer

probably in the archives). When calling the makeVennDiagram function you want to set the totalTest number to something that is larger than the experimentally determined peak number. As far as I know, the totalTest number is...by chance. So one way to sort this out using biological information is to think about the maximum number of possible binding events and use that as the totalTest number. …

ChIPpeakAnno ChIPpeakAnno

updated 15.0 years ago • Noah Dowell

to query biomaRt in batch mode. The PDF file available from biomaRt on-line pages shows a number of useful ways to extract useful data but it does not mention any batch interrogation mode. I thought R CMD BATCH would...each target gene transcript listed in data set hsTargets. Since I have to save to a file the miRNA identifier, the miRNA sequence, followed by all its target gene transcripts wit…

miRNA biomaRt miRNA biomaRt

updated 16.0 years ago • mauede@alice.it

4.0 MB) ================================================== downloaded 4.0 MB Error: Duplicate identifiers for rows (75, 83), (76, 84), (77, 85), (78, 86), (79, 87), (80, 88), (81, 89), (82, 90) Please suggest me the solution.     &nbsp

geoquery getgeo

updated 7.8 years ago • umahajan

div class="preformatted">Hi just to warn all users of the development version of biomaRt, please wait a few days before updating your RCurl, the current devel versions of these two packages do not...for the error that is produced, with RCurl_0.97-2 and biomaRt_2.1.0, is shown below. With a previous version of RCurl, the problem should not arise. library("biomaRt") mart = useMart("ensembl") e…

biomaRt biomaRt

updated 16.5 years ago • Wolfgang Huber

has 4 samples so totally 40 samples. If I am correct n.features should be = 3480 and the n.data (the number of samples that are present in each file) should be = 40. But reading in the file I've got the following error: raw <- readCtData...Ct"]]], ncol = n.data[i]) : data length [5765] is not a sub-multiple or multiple of the number of rows [145] any suggestions? thanks in advance, …

updated 13.2 years ago • alessandro brozzi

div class="preformatted">Hi, I came across a strange issue in 'knitr' with R code containing complex numbers entered directly using the "x + yi" notation. For an illustration see the minimal example: http://goo.gl/Yj77kI The sample...to get lost and what I get is: 1^2 ## [1] 1 Any ideas? Cheers, Andrzej [[alternative HTML version deleted]] </div

updated 12.2 years ago • Andrzej Oleś

D0, D1, D2 and D3. There were no replicates. Total 12 samples. We are trying to use edgeR to identify differentially regulated genes. Since edgeR doesn't give p-values without replicates, we took samples coming from...pair-wise comparisons between Control and experimental conditions at each dose, excluding D0, and identified overlapping genes. Now, we want to see the genes that have increasing…

edgeR DOSE edgeR DOSE

updated 12.4 years ago • Sandhya Pemmasani Kiran

Hi, i am trying to use FlowSOM to automatically identify cell clusters in a normal bone marrow sample. I managed to create the SOM however i experienced some trouble when...Error: FCS file found for sample Bue018 cfu normal 00000337 431.LMD has incorrect total number of events. Sample will be excluded. FCS not found for sample Bue018 cfu normal 00000337 431.LMD_720184 from searching...the file e…

FlowCytometryData FlowSOM Clustering FlowCytometry metaMSdata

updated 21 months ago • agustin

to compare each single sample to the rest, in order to find the interesting ones, then specifically identify which genes differ most from the population. I know it is not ideal to have no replicates, but I was thinking of fitting...9.50e-01 # Gene2 0.996 2.79e-11 9.96e-01 # Gene3 0.996 9.96e-01 1.68e-23 sessionInfo() # R version 4.4.0 (2024-04-24) # Platform: aarch64-apple-darwin20 …

limma DifferentialExpression

updated 14 days ago • jamie.gearing

div class="preformatted"> Dear Bioconductor community, I am looking for a package for Copy number analysis using CEL file that I have obtained from Affy SNP 6.0. I have CHP files from birdseed. Now I want to analyze my...data for Copy number and Loss of heterozygosity (using B allele frequency) and find regions of CN alterations and LOH with or without Copy...number changes. Can anyone dire…

SNP affy SNP affy

updated 13.7 years ago • Guest User

of freedom for each gene. The prior degrees of freedom are set to 20 by default, so the prior number of observations defaults to prior.n = 20/12 = 1.67 for your data. Try instead a smaller value like prior.n = 6/12. The smaller...if edgeR did this for you, adapting to the characteristics of your data automatically. A new version of edgeR should be able to do that in a few months. Best wishes…

Sequencing edgeR DESeq Sequencing edgeR DESeq

updated 13.4 years ago • Gordon Smyth

div class="preformatted">Hi, a substantially revised version of arrayQualityMetrics is available. It has a number of new features: - improved interactivity of the plots; expandable...users, especially on Windows). If you use the package, or want use it, it is worth installing the version from the devel branch, not from the last release, even on R 2.12.x. If you use R-devel (the future R 2.1…

GO arrayQualityMetrics GO arrayQualityMetrics

updated 14.8 years ago • Wolfgang Huber

<div class="preformatted">Hi, your not the first one. A few months ago I transfered a large data set via an external HDD and like you it took a long time to notice the fact that some CEL files were corrupt - some how the CEL files were still valid and read just file. It was just some probe intensities that had ridiculous large values. I used MD5 on the files to identify which files wer…

probe probe

updated 18.5 years ago • Henrik Bengtsson

Dear community, I tried to download data by using "TCGAquery_recount2". But, I found the number of sample is different using different functions in TCGAbiolinks. Why does this happen? Thanks a lot! If I used TCGAquery_recount2...the number of samples is 601 (542 Tumor and 58 Normal) for TCGA-LAUD. While it is 594 (535 T and 59 N) for TCGA-LUAD if I used "GDCquery", "GDCdownload...TCGAquery_…

TCGAquery_recount2 TCGAbiolinks

updated 4.6 years ago • xiaofeiwang18266

confused by my results: in the NGenes column (which is also the length of my`` index) ``, I got a number that is larger than the number of probes in my gene set. How can my probes match a larger number of indices than exist for...1]] ) is 11076 and l<code>ength (unique(gene.set [[1]] ) is 8873</code> <code># preparing the identifiers from biopsy experiment by extracting the en…

limma camera gene set testing

updated 9.6 years ago • claire.n.levy

Hello I am having trouble retrieving FASTA sequences for a some uniprot identifiers. It seems that in most cases this is due to the accession number now being a 'secondary accession number'. Is there...a way to retrieve sequences using these secondary accession numbers with uniprot.ws? Thanks -Brett

uniprot.ws

updated 10.6 years ago • bengelmann

with R yet, and I'm facing some problems while using DEseq for the analysis. In my institution the R version of the Linux servers system is 2.13.0 and the version I installed in my windows terminal is 2.15.2. I've retrieved multiple...DEseq manual versions from the internet (dated 19/01/2010, 21/04/2011 and 12/04/2012) , but some R commands vary from one to another and some are...not supported in…

DESeq DESeq

updated 13.2 years ago • José Luis Lavín

I am trying to use biomaRt with an archive version of Ensembl for reproducibility, since the project I am working on has specified a specific version of Ensembl (version...with the main Ensembl mart. Here is some example code to reproduce the error. I've used Ensembl version 100, which is the current version of Ensembl, to demonstrate that the error doesn't seem to have anything to do with the...…

biomart

updated 5.5 years ago • Ryan C. Thompson

of Freshwater Ecology and Inland Fisheries in Berlin. I am using your R package flowClust to identify coherent populations of microorganisms in environmental samples. The algorithm is performing very well however...but flowClust somehow do not exploit them. When I run it with K=1, it prompts "Using the serial version of flowClust"; while when set the number of cluster > 1 it uses two CP…

flowClust

updated 8.8 years ago • Jiang, Mike

<div class="preformatted"> Hi, I am using easyRNASeq for estimating the counts in an rna-seq alignment to hg19/GRCh37 done using bowtie2. I would like to get the counts "per gene". The code runs successfully and I get an output table, but the number of records in the output table are ~57000: cat count.tsv | wc -l 57774 I am wondering why the number of counts are so much greater than the …

GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt

updated 11.7 years ago • Guest User

I would like identify potential hybridization off-targets for a set of short DNA probes (16-20 nt) by detecting sequence matches across...max.mismatch, min.mismatch, : vmatchPattern() does not support indels yet sessionInfo( ) R version 4.3.0 (2023-04-21) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.3.1 Matrix products: default...BLAS: /System/Library/F…

Microarray Alignment Biostrings

updated 2.6 years ago • sandmann.t

when exporting your results to a file. Can you let me know if that explains the difference in number of transcripts you notice? Cheers, Steffen > Dear mailing list, > > I have recently observed a discrepancies in genome...by using the web service www.biomart.org I received ~48000 > transcripts for the same genome version and chromosomes. > > By compari…

biomaRt biomaRt

updated 16.1 years ago • steffen@stat.Berkeley.EDU

Hello, I am taking a large list of accession numbers from NCBI’s EST and GenBank databases and using biomart R package to query the the Ensembl mart and the human gene...Hello, I am taking a large list of accession numbers from NCBI’s EST and GenBank databases and using biomart R package to query the the Ensembl mart and the human gene Ensembl...This all works as desired except for I am una…

annotation biomaRt r

updated 6.9 years ago • Morgan Howard

error: <pre> > GO_results <- GO_analyse(eSet = minimalSet, f = "Treatment") First feature identifier in dataset: ENSG00000000003 Looks like Ensembl gene identifier. Loading detected dataset hsapiens_gene_ensembl...Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line 7 and …

goexpress

updated 9.7 years ago • martin.hoelzer