Bioconductor Forum

changes to the empirical Bayes calculations in limma since the early days. These have been in limma versions 2.4.0 and 2.4.13. The change in 2.4.0 was introduced to better handle the possibility of residual standard deviations...rma() can produce a subset of probe-sets with identifical expression values across samples when the number of samples is small (three or four), as an artifact of the sum…

Microarray limma Microarray limma

updated 19.6 years ago • Gordon Smyth

Hi  I am currently working on some metagenome data and I'd like to use DESeq2 tool to find the genes that are differentially abundant in different treatment over time. Due to the type of the study, I need to normalize the count data (genes abundance) per 16S rRNA copy number which changes the distribution and nature of data from count to decimal. I know that DESeq2 works on the…

deseq2 metagenomics

updated 8.3 years ago • ghanbari.msc

div class="preformatted">I have installed the newest version of annotation package rat2302, ver 1.8.5 . I have encountered what appears to be a discrepancy between the external...and internal package version information. The code that reproduces this is below. Am I looking at this wrong or is this an issue that can be addressed...Mark Mark W. Kimpel, M.D. > sessionInfo() R version 2.…

Annotation rat2302 Biobase reposTools affy Annotation rat2302 Biobase reposTools affy

updated 20.2 years ago • Kimpel, Mark W

I am using the `ComplexHeatmap` package to represent the intersection among different `GRanges`. The vignette has some nice example to plot it: library(circlize) library(ComplexHeatmap) library(GenomicRanges) lt2 = lapply(1:4, function(i) generateRandomBed()) lt2 = lapply(lt2, function(df) GRanges(seqnames = df[, 1], ranges = IRanges(df[, 2], df[, 3]))) n…

ComplexHeatmap

updated 6.8 years ago • Vinicius Henrique da Silva

Hi, I have RNA seq data with the samples defined as follows: **ID level stability type** A1 med unstable exp A2 med unstable exp A3 med unstable exp B1 med stable exp B2 med stable exp B3 med stable exp C1 low stable exp C2 low …

deseq2

updated 6.3 years ago • HD

I get a scan error if I use the version option in biomaRt while running latest R version 3.4.2.    <pre> ensembl <- useEnsembl(biomart="ensembl", dataset...hsapiens_gene_ensembl", version=90) ensembl@host [1] "http://e90.ensembl.org:80/biomart/martservice" getBM(attributes=c('ensembl_gene_id','external_gene_name...quote, dec = dec, : line 1 did not have 3 e…

biomart

updated 7.9 years ago • Chris Stubben

6265 ## 4 3 6233 ## 5 4 6291 ## 6 5 6357 ``` Which I assume is to make sure the number of ranges in each of the bootstraps is the same as in ``dhs``? When I exactly the same on my data, i.e. changing ``dhs`` to a GenomicRanges...seems like something has gone wrong. Is there a parameter that I am supposed to change to make the number of ranges in the bootstrap the same as in my t…

bootranges nullranges

updated 2.5 years ago • sam

trying to annotate some genes, eg. CEACAM6. My problem is as follows, Query input = chromosome numbers 1:22, Output attributes = ensembl_gene_id, unigene, chromosome_number,start_position,end_position,hgnc_symbol...attributes=a,filters='chromosome_name',values=1:22,mart=ensembl, verbose=T)->mydataset <?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query> <query count="0" d…

Cancer hgu133plus2 annotate affy biomaRt Cancer hgu133plus2 annotate affy biomaRt

updated 17.2 years ago • Julian Lee

to install DESeq2 but I had problem and it didn't work. An error tells me I need to upgrade my R version. but unfortunately every time I reinstall R it was 4.1.2 version, not 4.2.1. my operation system is Ubuntu 22.04 LTS

DESeq2

updated 3.2 years ago • yari.hadi

range of tissues. Even within a single cancer type such as breast cancer there can be multiple forms. Identifying subtypes will aid individualised treatment for improved survival and benefit the lives of those affected...by cancer. Cancer subtypes can be identified by analysing what genes are switched on/upregulated or are turned off/downregulated. Unfortunately, analysis...previously had success…

PhD clustering cancer Job

updated 7.7 years ago • Daniel Brewer

Hi I am wondering if I can apply "DiscoRhythm" for a very small number (5-10 ) genes detected by RT-qPCR to get an idea about Rhythmicy. I know the software is designed for large-scale data but

DiscoRhythm

updated 4.6 years ago • Do it!

for you) is to generate a text files containing a list of Homo-Sapiens validated miRNAs (microRNA- identifier, sequence) and relative 3'UTR regions (gene-identifier, 3'UTR-sequence). I realize this is just a matter of retrieving...regions ? 2) Function "hsSeqs" from package "microRNA" produces a matrix 709015x 6 contaiing miRNA identifiers and apparently some data from the paired gene. ex. …

miRNA Homo sapiens miRNA Homo sapiens

updated 16.5 years ago • mauede@alice.it

normal and cancer samples. Each samples contain mRNA microarray expressions. The final aim is to identify mRNAs that are significantly down/upregulated. What is the best R package we can use for this? - G.V. [[alternative HTML...version deleted]] </div

Microarray Cancer Microarray Cancer

updated 12.9 years ago • Gundala Viswanath

div class="preformatted">Hi, I was looking for a method to identify differentially expressed genes using the paired tumor/normal samples. Is there a method under DEseq to test for...such correlated data? Thanks, -Prabhakar Chalise [[alternative HTML version deleted]] </div

updated 12.3 years ago • Prabhakar Chalise

chromosomal coordinates for a region in using biomaRt or other BioC packages, how can I know the version of genome assembly being retrieved, and is it possible to define a particular version to use? eg, I am searching for 5...5utr", mart=ensembl) My questions: does it treat the start/end coordinates as in the latest version of builld 36 (2006)? can I opt for build 35 or hg17 (2004)? Thanks for…

biomaRt biomaRt

updated 17.1 years ago • Al Tango

at gmail.com > Fri Jan 31 21:58:26 CET 2014 > > Hi All, > > Is there a way to identify the genes that contribute to the gene set > enrichments calculated by roast/romer? I realize that all of the genes

updated 11.8 years ago • Gordon Smyth

div class="preformatted">Dear Madam/ Sir, I want install earlier version of Bioconductor (1.4 version ) on R-1.9.1. Is it possible to install earlier version of bioconductor by using getBioC...Or there is any other way to install earlier version of bioconductor. I try to install bioconductor using getBioC(), but I got following meaasge: Error in getBioC() : You are...currently running R ver…

updated 20.8 years ago • sachin Kumar

Hello, install.packages('impute') Warning message: package 'impute' is not available (for R version 3.0.2) May someone let me know how I could this problem? Thanks, Jerry [[alternative HTML version deleted]] </div

updated 11.7 years ago • Jerry Cholo

exon to width()-45. <pre> lapply(grl, function(x) resize(x[1],width(x[1])-45))</pre> However, a number of first cds ranges are less than 45nt. I could set up a number of conditions by segregating genes by the length of their

genomicranges genomicfeatures

updated 10.3 years ago • Jake

from Bioconductor. These packages are named org.<genome>.<id>.db, where <genome> is a short string identifying the genome and <id> is a short string identifying the gene identi_er. Currently, goseq will automatically retrieve...used genome/ID combinations." Let's say I want to use the organism package for the Apis mellifera version 2 genome, a supported genome according t…

GO Organism Apis mellifera goseq GO Organism Apis mellifera goseq

updated 13.8 years ago • Corby, Vanessa

Hello creators of ChIPQC, Could it be possible to have access to an older version of ChIPQC (version 1.31 for example) instead of the current version 1.32? ChIPQC worked great for me till I updated it...to the latest version. I got an error message described here: https://support.bioconductor.org/p/9144941/ I managed to downgrade R and use...an older version of ChIPQC I had on my machine (whic…

ChIPQC ChIP-seq DiffBind Rory_Stark

updated 3.4 years ago • etiennedanis

mgug4122a) Agilent microarray sets and I want to check if the methods I'm using make sense, as the number of significant p-values I'm getting seems quite high. I'm using Limma for the significance analysis. the lowest value...eBayes(fit2) my.lfc <- 0 output <- topTable(fit2, coef=1, adjust.method="BH", lfc=my.lfc, number = 20000) write.table(output, file="output.txt", sep="\t", quot…

Microarray Annotation limma Agi4x44PreProcess Microarray Annotation limma Agi4x44PreProcess

updated 14.1 years ago • Paulo Nuin

mgug4122a) Agilent microarray sets and I want to check if the methods I'm using make sense, as the number of significant p-values I'm getting seems quite high. I'm using Limma for the significance analysis. the lowest value...eBayes(fit2) my.lfc <- 0 output <- topTable(fit2, coef=1, adjust.method="BH", lfc=my.lfc, number = 20000) write.table(output, file="output.txt", sep="\t", quot…

Microarray Annotation limma Agi4x44PreProcess Microarray Annotation limma Agi4x44PreProcess

updated 14.1 years ago • Paulo Nuin

gt; From: "Jeremy Davis-Turak" <jeremydt at="" gmail.com=""> > Subject: [BioC] Limma: different numbers of duplicated spots > To: bioconductor at stat.math.ethz.ch > Message-ID: > <378b225b0704041451h72a7fbb3hc206614aec7cdc27...120 genes for the calculation of the consensus correlation? I read on this > list that small numbers of genes won't…

celegans celegans

updated 18.7 years ago • Gordon Smyth

will be biased towards sampleB? In other words can we compare two samples one having double the number of reads of the other? &nbsp

tmm normalised values

updated 8.8 years ago • manoharankumar01

div class="preformatted">Dear all, is there a possibility to download recent versions of bioconductor packages from the bioconductor homepage? I am interested in the marray-packages running under

updated 21.5 years ago • Sylvia Merk

DESeq2") then install as normal using biocLite. However, it keeps installing the older version of DESeq2 1.2.10 instead of the newest version. What am I doing wrong? Please help! Zach

deseq2 update

updated 10.9 years ago • zshao1

line up over the signal bars. I was checking this list for this problem and saw that HTqPCR release version is apparently up to version 1.1.0 whereas the bioconductor site shows 1.0.0. Maybe the new release would fix the problem...but where would I get it? Updating didn't change the version. I also am getting main bars of the form SD_myGroups, which I assume is standard deviation. Can I turn this…

HTqPCR HTqPCR

updated 15.6 years ago • Michael Muratet

amp;collection=all&tax_group=all&tax_id=10090&type=all&class=all&family=all&version=latest), it shows 542 records. How can it be so different? Kind regards, C

JASPAR2018

updated 6.5 years ago • capricygcapricyg

results of running the following in an R session sessionInfo( ) ``` Toop Loan customer Care number=9732430098//8658221735//♋call

InteractiveComplexHeatmap

updated 2.6 years ago • Udihvd

rely on is no longer available: `package 'ensemblVEP' is not available for Bioconductor version '3.16'` Looking in the repository listings, it appears that `ensemblVEP` lacks any source or binary packages in 3.16...What I need to know is: In a Dockerfile, what is the correct way to force Bioconductor to use version 3.15? My current approach is roughly: ``` RUN R -e " \ opt…

singularity ensemblVEP docker

updated 3.0 years ago • jtaylor-predicine

doesn't work anymore. I have updated my packages and R... Any clues how can I still query this version? What I want to do is work in hg18 coordinates, for this reason I am querying the archived db. Thanks, Adrian ensembl54...attributes", mart, verbose = verbose) : biomaRt error: looks like we're connecting to incompatible version of BioMart suite. > sessionInfo() R version 2.14.0 (20…

biomaRt biomaRt

updated 13.9 years ago • Adrián Cortés

div class="preformatted">Hi, I have 10 marker probe sets identified using Affy CDF (Hg 133A array). How can I find the corresponding probe set ID in the data normalized with MNBI entrez...CDF file? Thanks, -James [[alternative HTML version deleted]] </div

cdf probe affy cdf probe affy

updated 15.7 years ago • James Anderson

div class="preformatted">Failure to install on a fresh development/R version everything appears up to date: ###Check > source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org...is not exported by 'namespace:Biostrings'" in below > biocLite(c("GenomicFeatures")) Using R version 2.13.0 (R-devel), biocinstall version 2.8.2. Installing Bioconductor …

updated 14.8 years ago • Paul Leo

this function adds up the counts belonging to one biosample. I understand the meaning of this if the number of technical replicates per biosample is the same for all samples. Please tell me what should I do if the number of technical

DifferentialExpression RNASeq DESeq2 replicates StatisticalMethod

updated 4.1 years ago • poecile.pal

accounts for the experimental design. I have a table (ReadsPerGene_Meta) with 2 columns: 1. with the identifier for each sample 2. with the nature of the sample (a control or test). I then do as follows (in the code section) and it produces...an error. I understand that this error states that the number of rows in the design table does not match the number of columns in the counts table. Of…

DESeq2

updated 3.7 years ago • Adam

signs are used to indicate the the strand of the chromosome. The names give the chromosome number of concern. NA is assigned to probe identifiers that can not be mapped to any chromosomal location data at this time...correctly, the locations as in the affychipidCHRLOC > environments are given as chromosome number and base pair. How do I > interpret negative values in …

probe probe

updated 22.1 years ago • rgentleman

203.840215898533 ... 148 TZG_ARR_0003_x_at 48.7635207480323 ... ... As you can see, a number of probes have the same name but refer to different oligos. The number in front of the row is just added by me, therefore...2400 0 2046 2070 + 1 This should be the same area. In this received list, I can identify the unique probes using the 2 numbers right after the exclamation mark, whi…

probe probe

updated 14.9 years ago • Karsten Voigt

cloneID's from for example Human microarray 19K human ESTs and find out the corresponding accession number and subsequently Unigene identifier. I would like to keep a database of this information. I would also like to know if...download a file including information for all clones including IMAGE cloneID and Genbank accession numbers among other fields. My first goal in this project would be abl…

Microarray GUI annotate Microarray GUI annotate

updated 22.0 years ago • Law, Annie

Greetings, Although your website states that Bioconductor works with R version 3.2.2, I am unable to load it into R and keep receiving the following warning message: Warning message: package ‘BiocInstaller...is not available (for R version 3.2.2)  > biocLite() Any assistance you could provide would be appreciated. Thank you, Nicole Lee

R Bioconductor software error warning message

updated 10.1 years ago • nmlee

<div class="preformatted">Hi, My OS is Mac OS X Server 10.4.8 I've got a fully functional R-2.3.1/bioconductor instance and decided to try installing R-2.4.0 in a different location. the R-2.4.0 appears fine but the bioconductor packages dislike the kernel version. The error is: ----- Error: package 'affy' was built for universal-apple-darwin8.8.1 ------ my version is: #uname -a Darwin lu…

Biobase affy Biobase affy

updated 19.0 years ago • Charlie Whittaker

transfected with plasmid expressing P53 at 16h (Cy3) i.e. PR.Cy5 vs WT.EP+P53.16h.Cy3 I need to identify two sets of differentially expressed genes induced solely by the over-expression of P53 at 8h, and at 16h. I took the

limma limma

updated 17.7 years ago • Ng Stanley

expressed genes to the `GeneSet` function. Out of 147 - 82 genes are unmapped, and the number of unique genes across all the tissues is 29, which means that 36 genes are not present in the output object. Does it mean

TissueEnrich

updated 6.9 years ago • fshodan

Today I updated r to the latest version and it turns out that I am unable to install the 'goseq' package, which is necessary to perform my analysis. I get the message...package 'goseq' is not available for Bioconductor version '3.19'. I cannot change the bioconductor version to an older one, because the older ones are not compatible with the latest...version of R (4.4). in turn, when I try to run…

goseq

updated 19 months ago • Patrycja

How does one make Jupyter notebook use a specific version of R? - I have had some issues with running DESeq2 via Jupyter Notebook from Anaconda (https://support.bioconductor.org...p/118241/) - We recently downloaded a separate version of R from CRAN (not via Anaconda). This version has none of the problem we experienced with the version from Anaconda...However, we can not get Jupyter Noteb…

deseq2 software error

updated 6.8 years ago • david.wheeler7

Hi, I am having trouble installing the Bioconductor in my R-studio. My R-studio is updated (R version 3.3.1), I am using the newest version. When I type "source("https://bioconductor.org/biocLite.R")" in the console and hit enter...I get following message: "Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help A new version of Bioconductor is available after installing the most…

bioconductor rstudio

updated 8.4 years ago • yog312

Hello, I would like to identify the Differentially Expressed Genes (DEG) perturbed by a drug 'metformin'. The experiment is one-color microarray...Hello, I would like to identify the Differentially Expressed Genes (DEG) perturbed by a drug 'metformin'. The experiment is one-color microarray as...nbsp; 3. If I analyze the microarray by just considering ('cellLine'), then for MCF7, th…

limma cmap microarrays differential gene expression

updated 8.9 years ago • kevin.m.hao

most language agnostic as possible - right now we have a bunch of 'annotation dirs' organized with versions and/or download dates in pathnames which stores genomes, gene coords and so on in flat tab delimited files. Ideally...or converting some gene ids, etc) with a set of ad hoc R scripts. In this scenario the problem of version management arises: it's not only necessary to write somewhere t…

docker annotation pipeline

updated 9.5 years ago • Elena Grassi

pre> Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help BiocInstaller version 3.0 is too old for R version 3.2.0; remove.packages...BiocInstaller") then source("http://bioconductor.org/biocLite.R") A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install</pre...biocLite() ``) shows this: <p…

package updates

updated 10.5 years ago • Cataphractus

server but I can download packages so I don't think that is the issue. Many thanks John $ R R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051...affy_hg_u133_plus_2", : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attrib…

PROcess biomaRt PROcess biomaRt

updated 13.3 years ago • John Coulthard

invalid 'dimnames' given for data frame It has definitively to do with the selected identifiers, and I have the impression that made4 can not manage identifiers with an minus sign inside, such as: AFFX-HUMGAPDH...M33197_M_at AFFX-BioDn-3_at I am running ade4 (Version: 1.4-2) and made4 (Version: 1.8.0) under R 2.3.1 Has somebody an idea how to handle this problem? Thanks in advance, Heike

Classification affy made4 Classification affy made4

updated 19.0 years ago • Heike Pospisil

Hi - edit - i just re installed everything and it works now I have been using R version 3.2.4 'secure dishes', but it seems I have automatically updated to R version 3.3.0 beta 'Supposedly Educational' and...This error was very likely caused by R attempting to load packages from a different incompatible version of R on your system. Please remove other versions of R and/or remove environment vari…

software error

updated 9.7 years ago • chris86

Dear all, Is there any way to install specific version of the package apart from installing it from source? In particular is there any equivalent of `remotes::install_version

package

updated 4.5 years ago • zuljiamel1991

<div class="preformatted">I am getting error messages while using GOhyperG. The first is when I try to pass along a list of LL identifiers that has duplicate entries. I get a message that says that the list must be unique. This is solved my using the unique() function. The vignette, however, seems to say that the function automatically takes into account the non-uniqueness of the identifie…

Annotation rat2302 Annotation rat2302

updated 20.2 years ago • Kimpel, Mark W

40 untreated ) and more to come. This data tends to be heterogenous, so I am trying to have higher number of replicates to identify true biological signal. Now, as this is a paired design, there is no need to worry about the batch...of samples that behave differently ( due to various reasons like degradation, stress etc ) . So to identify different responses in the large panel of samples, I am d…

deseq2 eda sva rna-seq

updated 9.3 years ago • g.atla

I am trying to install Herper and it says it is not available for my version of Bioconductor. However, the Bioconductor website says that Herper should work with version 3.15 and R 4.2.1 which...require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) > BiocManager::install("Herper") …

3.15 4.2.1 Herper

updated 3.3 years ago • Melissa Anne

I would like to know what genome annotation version is used in MeSH.Bta.eg.db? In case I have a list of snps to map to genes before doing mesh analysis, I should make sure...the position (according to the genome annotation version of bos taurus) I need to use to make map coordinates instead of using the position set up in the snp_map provived with

mesh

updated 6.1 years ago • bsollero.bs

<div class="preformatted">Dear All, For a data set I am working on, besides ordering coefficients by "differential expression", we are interested in getting a quick idea of whether the variance of some genes is unexpectedly large. I thought about applying the expression in p.10 of the tech. report version of Smyth's "Linear Models and Empirical Bayes Methods (...)" (http://www.statsci.org…

Cancer Cancer

updated 21.6 years ago • Ramon Diaz

the org.Hs.eg.db and org.Sc.sgd.db. The org.Hs.eg.db has a mapping of ENSEMBL gene accession numbers to Entrez Gene identifiers, but the org.Sc.sgd.db completely lacks this and uses a mapping to SGD Gene Identifiers...I [31702, 31710] | 09 1 YAL062W 31568 32941 > sessionInfo() R version 2.11.0 (2010-04-22) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8…

Yeast ChIPpeakAnno Starr Yeast ChIPpeakAnno Starr

updated 15.5 years ago • Noah Dowell

Dear all, I would like to use the GOstats package under R version 3.6.0 following these guidelines: https://bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOstatsHyperG.pdf...hgu95av2.db") ``` I get this error message ``` package 'hgu95av2.db' is not available (for R version 3.6.0) ``` If anyone understands the problem, it would be very useful? Thanks Sarah

Go.db hgu95av2.db R3.6.0

updated 6.4 years ago • sarahqd