Bioconductor Forum

Illumina project runs. In theory, no genes should be differentially expressed. Nevertheless, edgeR identifies almost 7,000 genes as DE at a FDR rate of 0.1. This is very puzzling. I ran edgeR using the classic approach (exactTest...that could violate any assumptions made by edgeR? Is there any known problems with the newest version of edgeR? > sessionInfo() R version 3.0.2 (2013-09-25) P…

Sequencing RNASeq edgeR Sequencing RNASeq edgeR

updated 11.9 years ago • Blum, Charles

div class="preformatted">Dear Javier, oneChannelGUI uses apt tools for intensity summarization. In version 2.4 of Bioconductor gene-level expression was calculated using HuGene-1_0-st-v1.r3.mps file. In version 2.5 of Bioconductor...quite surprised with the results obtained. With oligo >package, after preprocessing with rma, the number of probesets are >253002 while with oneChann…

Preprocessing oneChannelGUI Preprocessing oneChannelGUI

updated 16.1 years ago • rcaloger

which are less peculiar (CN is still above and below 7 in some cases). I am naively trying to identify if this issue could be an artifact/bias or misstep in my implementation

Pure PureCN

updated 4.0 years ago • jacobgross04

div class="preformatted"> Dear All In regards to GenomeGraphs, is there a maximum number of transcripts per gene allowed? Amanda Miotto a.miotto at griffith.edu.au Software Engineer. Research Computing

GenomeGraphs GenomeGraphs

updated 17.3 years ago • Amanda Miotto

Outputing results... Error in data.frame(ASSIGN = "ASSIGN parameters", version = as.character(utils::packageVersion("ASSIGN")), : arguments imply differing number of rows: 1, 0 > sessionInfo() R version

software error assign

updated 5.4 years ago • yueli7

from the datasets. It's mentioned that batch can be detected from sample ID itself How do we identify the batch info from the sample ID? My ids look as follows. ``` TCGA-LL-A73Y-01A-11R-A33A-13 TCGA-AO-A03U-01B-21R-A10I-13 TCGA

TCGAbiolinks BatchQC BatchEffect

updated 2.7 years ago • snijesh

downloaded_packages BiocManager::install() ##: > BiocManager::install() Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2019-07-05) BiocManager::install(c("GenomicFeatures", "AnnotationDbi")) ##: > BiocManager...install(c("GenomicFeatures", "AnnotationDbi")) Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2019-07-05) Installing package(s) 'GenomicFea…

biocLite

updated 6.1 years ago • 3076782769

At 09:15 AM 10/14/2009, Likun Wang wrote: >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...etc, are all welcome. > Best regards >Likun > > [[alternative HTML version deleted]] > >______________…

Annotation DEGseq Annotation DEGseq

updated 16.1 years ago • Naomi Altman

I've tried to compare the output from Cellranger 3.0 with DropletUtils::emptyDrops() in term of number of cell-containing droplets. The web-summary from the Cellranger run outputs 1240 cells which is indeed very consistant...of the curve is around the 1100-1300th barcode). It is far less than I expected with regard to the number of cells I've put as input but this could be explain by some technic…

CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq

updated 3.8 years ago • gregoire.destreel

genome of a related ancestral species (that existed prior to the duplication event). I want to identify loci where the duplicates have significantly different expressions - I was wondering if I could use DESeq2 to do...r** indicates one of three replicates. I was then considering constructing a design matrix that can identify differentially expressed loci - for example conducting a log ratio …

rnaseq DESeq2

updated 2.0 years ago • pl23

div class="preformatted">I am working with Taqman Microrna and I am using different versions of cards. I am having problems with different version. Applied biosystem uses its own code that refers to specific...mirbase version. I wonder if you are aware of a database with relation between mirbase and taqman codes Thank you Marco </div

microRNA microRNA

updated 13.1 years ago • marco fabbri

I often need to retrieve number of samples or features of a given ExpressionSet. I use constructs like `dim(es)[[2]]`, and just to make my code easier to read

expressionSet

updated 5.6 years ago • aush

Hi, I use RUVSeq and I find it extremely helpful.  I have a question concerning the number of covariables to be used under RUVr. I've realized that increasing the number of covariables makes the groups I want...to see on the PCA more visible and distinct from each other. It follows the the number of DE genes also increases with k. In one of my projects I have 72 samples a…

rnaseq ruvseq RUVr edgeR

updated 10.0 years ago • David Rengel

hierarchy generated in OpenCyto. My problem is that I can't seem to find a way to control the number of decimals in gate labels. Default seem to be 3 numbers from the first non-zero number. Thus, in a gate the geom\_stats label

ggcyto

updated 9.0 years ago • anders.tondell

<div class="preformatted"> Hello all, I saw a couple of emails on the list with this problem regarding Illumina BeadChip Mouse-6 data. My problem is that for some probes I end up with only a nuID, with no mapping to the manufacturer's TargetID or ProbeID, and no transcript annotation. In some cases the annotation file from Illumina's web page would allow me to fill in this missing annotati…

Annotation lumiMouseV1 annotate lumi Annotation lumiMouseV1 annotate lumi

updated 18.3 years ago • Cei Abreu-Goodger

hsa-let-7a`$`9180` [1] 757 $`hsa-let-7a`$`9180` [1] 757 I would like to understand what is the number apparing on the same line as the miRNA identifier, following the "$" sign. ($`1588`, $`599`, $`9180`;....) It must be an index into something...Does this coordinate mark the beginning of the matching region ? What about the following list of numbers ? For instance: [1] 125 1107 [1] 1240 [1] 75…

miRNA miRNA

updated 16.3 years ago • mauede@alice.it

gt; get("1726_at", env=hgu95av2ACCNUM) [1] "HG919-HT919" Is "HG919-HT919" really an accession number? I do not get any hits at NCBI's GenBank. NetAffx gives the same identifier for that probeset, but in a field called "Representative...with "HGXXX-HTXXX" as ACCNUM on the hgu95av2 chip. Where can get more information about this identifiers? Thanks, Hans-Ulrich </div

Annotation Annotation

updated 18.4 years ago • Hans-Ulrich Klein

the data. Using the function depmap_copyNumer() results in the wrong table…not getting the copy number data…I think it is the metadata table…so maybe wrong linked. Cheers, Danny

software error depmap

updated 4.6 years ago • DannyM

I am trying to estimate sources of heterogeneity in methylation data in addition to some known sources (i.e., I have batch and age but would also like to correct for smoking, unmeasured technical artifacts, and cellular heterogeneity). When I use num.sv and the default "be" method, I get 12 SVs; when I specify the "leek" method, I get 0 SVs. Is there a reason why the two methods might behave so d…

sva num.sv

updated 8.4 years ago • brhead

through the mailing list since it may be of general interest. On the bioconductor page, there are a number of data packages, such as hgu95a, hgu133a. Among other goodies, they contain XDR files with environments full of mappings...from Affymetrix probe set identifiers to Unigene cluster IDs. For example, these may be used to figure out which probe sets from the same, or from different...Since the…

probe safe probe safe

updated 23.2 years ago • Wolfgang Huber

datasets each (presumably randomized and non-randomized expression matrix) and I am wondering how to identify them? How to confirm they're indeed in there and, if yes, extract them? I tried importing the FCS file with `` flowCore::read.FCS

flowcore flow cytometry dataset

updated 7.5 years ago • vinko.tosevski

I am reproducing a differential exon usage analysis using DEXSeq that was done on a previous version of the human reference genome (not sure which) with respect to the one I am using now (ensembl release 111). The previous...version reports 36 exons for my gene of interest (myo6), while the one I am using reports 73 exons. The exons I am looking for in silico...events versus the 500 outputted …

DEXSeq

updated 19 months ago • Alessia

<div class="preformatted">Hello, Does anyone know if there is a limited number of levels for a factor or how to reset the defaults? I have a two factor experiment which one factor has 2 levels while another has 7 levels. I got errors while I run following analysis. Please help. Thanks, Steve > design <- model.matrix(~phe+tr) > design (Intercept) pheVehicle tr1-…

updated 15.3 years ago • steve shen

Hello I used DESeq2 on RStudio version 3.2.3 about 3 years ago How can I found out which version of DESeq2 was used? Thanks

DESeq2

updated 4.1 years ago • adeler001

R-3.5.2 and I need R-3.4.2 to install certain genomic libraries. Is there a way I can run both R versions? How do i change the R version to use

R bioc

updated 6.8 years ago • pawan12394

as the `` p.values `` of the 3 pairwise contrasts. So far, so good. However, I assumed that the number of significantly genes identified by the F-test should equal the number of genes identified in any of the 3 contrasts...but I noticed this is not the case: the number of genes identified by the F-test is 3422, whereas this number for any of the 3 contrasts is much larger, namely 4438. Again...I…

limma

updated 7.6 years ago • Guido Hooiveld

<div class="preformatted">Dear all, I would like to ask which is, at the moment, the most popular method to identify differentially expressed genes for two colour cDNA microarrays. Is "limma" the method that one would "trust" more in...preformatted">Dear all, I would like to ask which is, at the moment, the most popular method to identify differentially expressed genes for two colour c…

limma limma

updated 19.4 years ago • E Motakis, Mathematics

data set, in a single GEO file (GSE20574), from an Agilent 244A aCGH array. My primary goal is to identify deleted, normal, and gain/amplification regions on all chromosomes, and then to identify genes annotated to these...like this before, I'd be grateful for advice. Looking at the bioc package repository, I see a number of CGH-related packages, but I am not quite sure which to use. What do I…

aCGH CGH aCGH aCGH CGH aCGH

updated 15.1 years ago • Paul Shannon

<div class="preformatted">Thank you, Jim. One more question. The eBayes step adjusts the variance across genes. Since there is already a good estimate for the variance due to the large number of samples does the eBayes step shrink the variance even further? Thank you, Giovanni Hi Giovanni, On 4/28/2014 8:54 PM, Giovanni...the variance across genes. Since there is already a good estimat…

updated 11.6 years ago • Giovanni Bucci

the last week biomaRt error :: The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing...list. All attributes appear valid. I have also tried subsetting on a smaller number of attributes without success. Advice, input and resolution welcome. Cheers. Ashley …

biomart number of columns in the result table does not equal the number of attributes in the query

updated 8.0 years ago • ang

find DE genes. But I do not understand why even when the bam files and references are the same the number of genes are different in the result of cuffdiff and HTseq. Actually I expected to have different number of counts for...each gene but not getting more (nearly 100) number of genes in HTseq comparing to cuffdiff. Thank you in advance</div

updated 13.0 years ago • Fatemehsadat Seyednasrollah

have used DESeq to perform a pooled comparison between the normal and cancerous samples and find a number of genes that are differentially expressed. We would also like to perform a paired analysis (simple comparison between...the two tissue samples from the same individual). Our logic is that the pooled analysis will tend to identify genes as differentially expressed only if they are fairly con…

Cancer DESeq Cancer DESeq

updated 14.5 years ago • Timothy Hughes

how to obtain the download number of a Bioconductor package quickly, instead of summing the download number per years in the stat webpage? just like a...bioconductor.org/packages/stats/bioc/DESeq2/DESeq2_stats.tab` could be used to calculate the total number. Seems no API did this sum. added: `https://github.com/r-hub/cranlogs.app/issues/43

badges

updated 3.4 years ago • zhilongjia

Sorry for the stupid question, I'm totally a baginner in cDNA data Analysis... Can I derive the number of wells in a plate from a .gpr file ? I would like to use it for the normalization... I looked in the web and in the mailing list

Normalization Normalization

updated 19.7 years ago • Giulio Di Giovanni

Dear All, I installed R version 3.2.2 on our server, and tried to install Bioconductor version 3.2. However, no matter what I do, I always got the following...error:  <pre> > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help BiocInstaller version 3.0 is too old for R version 3.2.2; remove.packages...BiocI…

bioconductor

updated 10.0 years ago • Jeff Zheng

I ran DESEQ2 with the raw counts of protein coding genes from my total RNA sequencing experiment to identify my DEGs. I understand that when doing PCA, its better to transform the normalized data to the log2 scale, either rlog...outlier identification. However, DESeq2 also suggests going for rlog rather than when you have small number of samples (>30) and vST for large datasets (hundreds…

DESeq2

updated 2.4 years ago • nisreen.khambati

Hi! I am using DESeq2 on an in-house server which is shared among a handful of users and has not a cueing system. I want to set a limit on the number of nodes DESeq2 uses, for which I used `MulticoreParams` as follows: ```r parallelParams <- MulticoreParam(workers = 4,progressbar = TRUE, log = TRUE) register(parallelParams,default=TRUE) parallelParams ``` Which prints the fo…

DESeq2 BiocParallel

updated 3.1 years ago • Sebastian

an initial selection of hits? I am also working on a sensititzation screen, where I am trying to identify genes that are differentially knocked down. This problem seems analogous to microarray studies and in that vein...I need to perform multiple test corrections on the p-values - does the 'multiple' refer to the number of conditions in which the assay is run (drug and no drug) or the number of …

updated 16.4 years ago • Rajarshi Guha

<div class="preformatted">I am using the GSA package for gene set analysis. I have normalize data from a microarray experiment with four groups and four replicates (16 total arrays). I downloaded the set of curated gene sets ("c2.all.v2.5.symbols.gmt") from the Broad Institute web page MSigDB (I did register) and read the data into R using the GSA package as follows: geneset.obj&lt…

Microarray Microarray

updated 16.2 years ago • Alexander C Cambon

Warning messages: 1: In myrows[i] <- which(Age_LNGSVsISS.topTable.2k[, "mappings.Sub.ENTREZID"] == : number of items to replace is not a multiple of replacement length 2: In myrows[i] <- which(Age_LNGSVsISS.topTable.2k[, "mappings.Sub.ENTREZID...number of items to replace is not a multiple of replacement length 3: In myrows[i] <- which(Age_LNGSVsISS.topTable.2k[, "mappings…

GO hgug4112a GO hgug4112a

updated 16.1 years ago • Massimo Pinto

Dear Bioconductor community, based on a project, trying to identify damaging somatic alterations per patient, I was trying to annotate some selected CNAs with their respective total...copy number, to obtain the relevant annotated genes; On this premise, I tried to use the CNVRanger R package and proceed as follows...r head(ex.dt) # the input data frame of selected copy number annotations based…

CopyNumberVariation CNVRanger GenomicRanges

updated 3.8 years ago • svlachavas

<div class="preformatted">Dear All, first I would like to apologize for a long mail. I am working with probe profile file(tab separated file) generated by illumina beadstudio software. Main objective is to identify differentially expressed genes. the experiment is done using single channel illumina microarray data. There are...profile file(tab separated file) generated by illumina beadstu…

Microarray probe limma Microarray probe limma

updated 16.3 years ago • Md.Mamunur Rashid

div class="preformatted">How I determine the version of a bioconductor function I am using? I installed the hexbin function using getBioC some time ago. Now I am writing...up a manuscript and would like to cite which version I used.</div

hexbin hexbin

updated 21.7 years ago • Obi Griffith

Hi, I'm trying to use ensemblVEP with version 78 of the Ensembl API. It seems that the package doesn't support version 78 yet. Are there any plans to include support...for version 78 soon? It seems that a new option that was introduced in version 78 of the API is causing ensemblVEP() to fail. Here is...path(con)) : file(s) do not exist: '/tmp/RtmpYsB9y8/file2c6244d9bfdd' Enter a frame numb…

ensemblvep

updated 11.0 years ago • Moiz Bootwalla

Hello! I have identified 4 clusters in my sce object and would like to know the cell IDs in a particular cluster. I know the > table(sce$clusters...Hello! I have identified 4 clusters in my sce object and would like to know the cell IDs in a particular cluster. I know the > table(sce$clusters) command shows me the number of cells in each cluster, however I can't work out how to …

SingleCellExperiment cluster identities sce

updated 5.6 years ago • reinepapillon

<div class="preformatted">Hi, I have a question about concerning the number of differentially expressed probes after batch combination, using ComBat from 'sva'. I have 2 data sets: one containing around 250 samples that correspond to around 50 groups, another one containing 10 samples corresponding to 2 groups (let me call them Batch2_Group1, Batch2_Group2). One of the 2 group labels in t…

updated 12.5 years ago • Michaela Oswald

T2_S2_drought (8 columns), performed the comparison and got 23 DEGs. I am wondered that Why the number of the columns uploaded to the Deseq2 affected the number of DEG. Note that the reported DEGs seem to involved in the

deseq2

updated 6.9 years ago • naktang1

to tell the functions which one should be. but it still works can you tell me which function can identify them. such is the coding: reads <- readFastq(fastqfile); qual <- FastqQuality(quality(quality(reads))); #qual <- PhredQuality

cycle cycle

updated 13.2 years ago • wang peter

nbsp;3    0.169999731 and i know A=1 , B=2 and C=3 then how i can replace the number with A , B and C???? thank u &nbsp

software error R

updated 9.8 years ago • Angel

To the developers, I'm using DESeq2 version 1.14.1, and I want to upgrade to version 1.16.1, but I'm still stuck with version 1.14.1 I'm using R version 3.3.2 and Bioconductor...I can't get the version 1.16.1. Also, you mentioned on one of the threads that "<span style="background-color:rgb(245, 245, 245)"> "lfcShrink() gives...the identical moderated LFCs as DESeq() gave in prev…

deseq2 betaprior=true lfcshrink

updated 8.3 years ago • tarun2

Hello, It might be a silly question, but I am struggling with it all day now. Hopefully someone with bright insight may be of any help. I have this df which contains a column with ID names. Some ID names occur one time, other two, and some even 20 times. In other words some IDs are in 1 row, others in many rows. What I would like to make is a new column which numbers the replicate IDs (from 1,…

plyr

updated 10.2 years ago • b.nota

We performed RNA-seq with cell number normalised ERCC-spike/Loess normalisation in which shows a global shift in gene expression. Is DESEQ2 appropriate...to be used in this context to identify DEGs and how would the normalisation be performed

DESeq2

updated 4.1 years ago • Ron

file only has ensembl gene and transcript IDs for each spot; in addition since the chip was made, a number of the genes on it have been removed from ensembl as they were incorrectly identified or thought to be bacterial contaminants...b) link gene ontology information to all the genes on the array that are still listed in the current version of the ensembl database. Appologies if this is a relat…

GO annotate limma GO annotate limma

updated 19.8 years ago • Amy Mikhail

to do this task I received this: Warning message: package ‘biocLite’ is not available (for R version 4.0.2) I have already downloaded ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager...BiocManager::install(version = "3.12") BiocManager::install("biocLite") BiocManager::install() ``` Do you know when I could install `biocLite` at R.4.0.2? …

biocLite

updated 5.1 years ago • jmagomez

KEGG and Reactome. When using the default ontologies or KEGG, the function `getgo()` can be used to identify the differentially expressed genes in each enriched pathway. However, `getgo()` does not support Reactome, so I'm having

goseq go rna-seq

updated 5.7 years ago • hasse.bossenbroek

as opposed to reads not mapping to any of the annotated features.) Is there an easy way to get this number? I was thinking of counting again, this time with inter.feature=FALSE and subtracting the results, but this is not quite...The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. </div

updated 11.6 years ago • Gabriele Schweikert

I am having problem downloading DESeq2_1.3.44.tar.gz using the gz folder. I am using R studio version 3.0.2. Here's the error message I received: * installing *source* package 'DESeq2' ... ** libs *** arch - i386 ERROR: compilation failed...DESeq2_1.3.44.tar.gz??? had non-zero exit status When I tried installing using the command lines, version 1.2.10 was installed. Is the 1.3 version ready for…

updated 11.8 years ago • Guest User

I have a MacBook Pro with an M1 chip. I have updated to the latest version of bioconductor (v3.15), however I am unable to install bioconductor packages due to compilation errors. As the documentation...says this version is built/requires R v4.2, as such I updated and my current R set-up is: ```r R version 4.2.0 (2022-04-22) Platform: aarch64-apple...under: macOS Monterey 12.3.1 Matri…

biocmanager R gofortran Bioconductor

updated 3.6 years ago • Olivia

I am interested in counting the number of reads that span splice junctions. Therefore, I set the options GTF.featureType = "transcript", useMetaFeatures = FALSE...are duplicated. What combination of parameters should be used to make the row names be transcript identifiers? Also, the counts\_junction data frame has no feature identifiers, just NAs in the first two columns with these

rsubread featureCounts

updated 9.1 years ago • Dario Strbenac

file have a match with a gene ID from the "org.Ssalar.eg.db" package. I have run the command in R version 4.3 and 4.5.1 (which is the one I currently have) and with AnnotationForge version 1.44 and 1.5, and in both scenerios...prefix = "SalmonChip", probeFrame = probeFrame, orgPkgName = "org.Ssalar.eg.db", version = "1.0.0", maintainer = "name <name@mail.com>", author = …

AnnotationForge

updated 4 months ago • Jaqueline