Bioconductor Forum

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

div class="preformatted">Hi Is there a way to convert non-HUGO gene symbol identifiers to entrez gene or other ids? Example: ACSL1 aka ACS1; LACS; FACL1; FACL2; LACS1; LACS2; ACSL1 Thanks in advance -burak...alternative HTML version deleted]] </div

convert convert

updated 17.1 years ago • burak kutlu

data for affy oligonucleotide microarray data . How can I read the data into R ? and how can I identify the upregulated and downregulated genes ? [[alternative HTML version deleted]] </div

Microarray affy edgeR Microarray affy edgeR

updated 13.3 years ago • Shravanthi P

working with data coming from deep sequencing of 48 small RNAs libraries and using edgeR to identify DE miRNAs. I could not figure out how to design my matrix for the following experimental design: I have 2 varieties...in 4 physiological stages. None of them represent a control treatment. I'm particulary interested on identifying those miRNAs which modulate their expression dependent on genotype…

Sequencing edgeR Sequencing edgeR

updated 13.2 years ago • Danie

p-value, should all of them be select for GSEA, or there is a rational way of choosing the number of DEG for GSEA

GSEA DEG

updated 9.8 years ago • Shamim Sarhadi

I ran DESeq on this subset. After I ran the two analysis approaches, we have observed that we identify an higher number of DE genes using the DESeqDataSet that includes the 4 conditions (174 DE genes) than when we perform

DESeq2

updated 4.1 years ago • giulia.lopatriello

ID in each table cell, which should be the best one, as they are sorted according to the total number of identified peptides? OR 2. Is it better to take all protein IDs in each table cell? This way we are accounting for simultaneous

Proteomics enrichment Perseus

updated 5.8 years ago • harelarik

<div class="preformatted"> Hello all, I have a question while I am using the limma package to identify differentially expressed genes: should I perform gene filtering after normalization to exclude genes that are likely unexpressed in the samples before fitting the linear model. With my limited stats knowledge, I believe the inclusion of 'unexpressed' genes may affe…

Normalization affy limma Normalization affy limma

updated 16.2 years ago • Peng, Fred

will be a reasonable threshold? I’m sure that for many experienced people doing DGE it should be a number that is sounded as a correct a safe threshold.  I will like to have some advice regarding this question. 2. I understand...that DESeq2 perform independent filtering, and that for this purpose it identify a threshold base in counts and remove genes that given the counts cannot produ…

deseq2 independent filtering lowcountgenes

updated 9.8 years ago • colaneri

I am using a dataset that was annotated using Ensembl version 87 of human reference genome version 38. I wrote an R script to access certain values for that data (FASTA sequences...I am using a dataset that was annotated using Ensembl version 87 of human reference genome version 38. I wrote an R script to access certain values for that data (FASTA sequences for the protein-coding genes). However …

biomaRt ensembldb RNA ensembl

updated 2.7 years ago • Christopher

div class="preformatted">hi; I am wondering what versions of: "miranda","mirbase","mirtarget2","pictar","tarbase","targetscan" are provided by the current version of 'RmiR.Hs.miRNA

updated 12.2 years ago • Hamid Bolouri

Hi, My workstation is running Debian 10 with the default version 3.5.1 of R. I need to use the Bioconductor package "GoSeq" to perform functional enrichment tests as described in “Running...trinityrnaseq/wiki/Running-GOSeq). I got a trouble with it. The package "GoSeq" exists only for “R version "3.6" in Bioconductor Release 3.10 which works with R version 3.6.0. After updating the R to the l…

goseq installation

updated 6.0 years ago • gdalsky

div class="preformatted">Hi, I tried to install the new version 1.4, however, noticed that neither the default (getBioC() ) nor explicitly calling getBioC("cdna") would install the vsn

vsn vsn

updated 21.5 years ago • Hinnerk Boriss

1)</code> Looking for the genes with maximal fold changes in the size factor-normalized counts identifies a large number of very similar genes (i.e. names identical apart from a number, no difference in description on GeneCards

deseq2 rnaseq differential gene expression

updated 9.8 years ago • willmacnair

Hello, I encountered a rare problem with segment() in the DNAcopy package. Specifically I see artifactual segments with ouptut$loc.start greater than output$end.start and output$num.mark=0 and output$seg.mean=NA. In my case, it seems to be caused by "chromosomes" (contigs) with empty copy number data point (NAs). Here is a minimal example to try and illustrate the problem:   <pre&…

DNAcopy dnacopy

updated 8.4 years ago • Alexandre Kuhn

<div class="preformatted">I am running R 1.5.1 and I have installed the affy package version 1.2.1. When I start R and select library affy I get the following error. Any help? Isaac P.S. I have installed HDF5 and rhdf5...div class="preformatted">I am running R 1.5.1 and I have installed the affy package version 1.2.1. When I start R and select library affy I get the following error. An…

Normalization rhdf5 tkWidgets affy Normalization rhdf5 tkWidgets affy

updated 23.3 years ago • Isaac Neuhaus

div class="preformatted">Hello, BioC folks I wonder whether there is a way to retrieve the total number of human genes annotated in Pathway of REACTOAM, one biomaRt mart. Thanks a lot! Gilbert </div

biomaRt biomaRt

updated 15.7 years ago • Gilbert Feng

According to the Bioconductor web page for DMRcate, it looks like it is available for Bioconductor version 3.18 but this installation fails: ```r > BiocManager::install("DMRcate") Bioconductor version 3.18 (BiocManager 1.30.22...package(s) 'DMRcate' Warning message: package 'DMRcate' is not available for Bioconductor version '3.18' A version of this package for your version of R …

DMRcate

updated 2.1 years ago • Daniel E. Weeks

Dear Bioconductor Maintainers: I encountered a version conflict when trying to push updates to scQTLtools: Push modifications today but was rejected, so I used "--force" and...received error: ```bash "Error: Illegal version bump from '1.1.0' to '0.99.14'." ``` but Bioconductor website shows version 0.99.12 (matches my local version before modification...Question**: Why does the remote …

Bioconductor

updated 8 months ago • XFWu

command. BiocManager::install("xcms") BiocManager::install("MSnbase") I noticed the version I installed through this command is not the latest release version of these two packages. I am not sure if this is the...developers issue or the *install()* function does not refer to the latest version. For now, I just manually download the tgz file to install the latest version. Can any…

debug BiocManager R pacakge R mass spectrometry

updated 6.1 years ago • wang.lingjue

Seq data which i mapped and used tophat for mapping splice junctions,I would like to use EdgeR for identifying differentially expressed genes. Do you have an idea if i can use tophat out put file as input for edgeR? Best Regards...Asmaa [[alternative HTML version deleted]] </div

edgeR edgeR

updated 12.8 years ago • Asma rabe

advice on how best to generate this myself. Thank you. Regards, Adai [[alternative HTML version deleted]] </div

Annotation Annotation

updated 12.2 years ago • Adaikalavan Ramasamy

<div class="preformatted">Hi All I am trying to use crlmm package for doing the genotyping and CNV analysis on a set ~200 samples genotyped on Illumina Omni5 array. I tried following the vignette (seems a bit dated) and got some errors(see below) http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst /doc/IlluminaPreprocessCN.pdf Also searching a bit more I found multipl…

SNP Annotation Normalization crlmm copynumber SNP Annotation Normalization crlmm

updated 11.9 years ago • Abhishek Pratap

pre> <pre> Warning in install.packages : package ‘MacroCAIC’ is not available (for R version 3.1.2) > install.packages("CAIC")</pre> <pre> Warning in install.packages : package ‘CAIC’ is not available (for R version

phylogenetic MacroCAIC

updated 9.9 years ago • Gabi

div class="preformatted">Hi, Can one access builds of old versions of bioc packages? For example, is it possible to get and install all versions of e.g. 'Rsamtools' that have at any point

cycle cycle

updated 12.6 years ago • Julian Gehring

Hi, Trying to install TCGAbiolinks, which has version 1.2.3 of SummarizedExperiments.  When I install via biocLite(), I get version 1.0.2.  I tried checking out the...there. I also tried removing the package and reinstalling it, with no improvement.   R version: 3.3.1 Bioconductor Version: 3.2   What am I missing? Any help would be nice, Gaius

summarizedexperiment

updated 9.3 years ago • gaiusjaugustus

I have some RNA-seq samples from mouse, 2 conditions with 4 replicates each, read quality is good and for each sample 85-90% of reads align. The number of aligned reads in millions are: Condition 1 replicate 1: 100 Condition 1 replicate 2: 79 Condition 1 replicate 3: 52 Condition...with 4 replicates each, read quality is good and for each sample 85-90% of reads align. The number of alig…

deseq2

updated 8.2 years ago • Mike

like to use the qAlign function in QuasR. However, I do not see any parameters for specifying the number of mismatches allowed (-v parameter in bowtie) or the number of alignments (-k parameter in bowtie) to output for a multi

QuasR

updated 6.0 years ago • Julie Zhu

<div class="preformatted">Hi Al, The current version of lumiHumanAll.db was built based on Illumina Company provided annotation files. As the probes were designed based...div class="preformatted">Hi Al, The current version of lumiHumanAll.db was built based on Illumina Company provided annotation files. As the probes were designed...Human WG6 chips, and lumiHumanAll.db. After > …

Annotation Clustering probe convert Annotation Clustering probe convert

updated 17.6 years ago • Pan Du

BiocManager") > > BiocManager::install("illuminaHumanv4.db") Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignette

Bioconductor Annotation Ann

updated 2.3 years ago • Aytaç

I asked my question to Affymetrix support and they answered: This difference can be due to a number of reasons. Firstly, the CDF file is the array layout information designed for 3' IVT array analysis, and are therefore...Thank you, Sophie LAMARRE Biostatistician - Toulouse (FRANCE) -- output of sessionInfo(): R version 2.13.0 (2011-04-13) Platform: i386-pc-mingw32/i386 (32-bit) locale: […

Annotation cdf probe Annotation cdf probe

updated 14.0 years ago • Guest User

need to extract biologically relevant results at single patient level. For context, we have a big number of brain tumours but due to the delicate structure of the brain and funding, we do not have the capacity for biological...the expression of multiple brain tumours with a certain classification to that of normal tissue and identifying significant results. However, in the process of making in…

GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod

updated 2.1 years ago • Manthos

But I get the following error: ```{r} Error in `[.default`(tab, , 1) : incorrect number of dimensions ``` I'm not sure if this is a bug or I am doing something wrong. I would be most grateful if you could shed some

GOstats GO R

updated 5.5 years ago • ramonmassoni

Enter the body of text here I did RNAseq of a Drosophila cell line. By using RNASTAR in Galaxy I am getting high number of reads mapped to too many loci. (uniquely mapped 60 %, mapped to multiple loci 10 %, mapped to too many loci 24 %). Later when I...text here I did RNAseq of a Drosophila cell line. By using RNASTAR in Galaxy I am getting high number of reads mapped to too many loci.…

RNASeqData

updated 3.8 years ago • vasa.broz

I use a cell line, in which, as all in vitro cell-based experiments, the passage number will affect the gene expression (the influence of the passage number is well-known and accepted in literature). I have...N=2 (which N=the biological replica that corresponds to passage number). Each N has 1) control, 2) substance A, 3) substance B, and 4) substance C (total number of samples=8, 4 for each pa…

DESeq2 passagenumber

updated 3.3 years ago • swn281

Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version 3.0.0. Installing package(s) 'hthgu133pluspm.db' Warning message: package ???hthgu133pluspm.db...is not available (for R version 3.0.0) Code: # CREATE GeneSetCollection library(GSEABase) x <- scan("GeneSets.gmt", what="", sep="\n") GeneSets.gmt <- strsplit...var.filter=FALSE, var.cutoff=0.25, filterByQuantile=TRUE, …

GSVA GSVA

updated 12.7 years ago • Guest User

We have a project running in version 3.4.4 of R. When we build it, we are getting an error that BiocInstaller is not available (see below). According to https...on what could be causing this or what we could try differently? We'd like to avoid upgrading our version of R if possible. Code should be placed in three backticks as shown below ```r > source("https://bioconductor.or…

BiocInstaller

updated 3.5 years ago • Kevin

I am attempting to extract copy number from EPIC and EPICv2 arrays. I have tried some things but run into the same issues as reported [here](https://support.bioconductor.org

conumee CopyNumberVariation MethylationArrayData

updated 10 months ago • Adam

Hello, I would like to use coseq to cluster my results based upon transcripts that were identified as differentially expressed by DESeq2. Coseq mentions that I can take the object (e.g. dds) and use that directly...must be one of the following: none, TC, DESeq, TMM, or a vector oflength equal to the number of columns in ‘y’ ``` Looking at the code, I did specify a valid option …

coseq rna-seq

updated 6.8 years ago • varunorama

I am trying to benchmark methods for detecting cell outliers. Although it is not very meaningful to identify a very small number of outliers in scRNA-seq datasets that usually contain thousands of cells, it may be a straightforward

splatter simulation

updated 7.6 years ago • luke.zappia

two scRNA-seq datasets, both derived from a heterogeneous population of cells (comprising similar numbers of cell types and subpopulations). One sample has been treated with a drug, the other has not. While I can separate out...the cellular subpopulations in each dataset, what I want is to then identify differentially expressed genes that result from the drug treatment - in each of the individual…

scrna scrnaseq differential gene expression

updated 8.2 years ago • d.depledge

Hi, I changed to R version 3.2.0 and DiffBind version 1.14.3. The problems are: - The heatmap produced by data = dba(sampleSheet="HistoneData\_C.csv...minOverlap=2) plot(data) is different that in previous version that I had (1.8.5) (grouping of samples is different). Is this because of a change in the method or a bug? I tried several...versions of parameters. - The side colours in heatma…

diffbind new version

updated 10.6 years ago • pkra

div class="preformatted">Hello I am tryng to install GenomeRanges in R, svn last version, but the required version of IRanges is not available (1.13.23). Details are below. Thank you in advance > biocLite("GenomicRanges...BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.3.7. Installing package(s) 'GenomicRanges' Installing package(s) into '/stockage/…

IRanges BiocInstaller IRanges BiocInstaller

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updated 2.6 years ago • yakes61237

and hope to seek suggestions on completing the analysis within 1 to 2 months. The objective is to identify differentially expressed genes, and to perform gene ontology analysis. Now I am at a loss given the diverse packages...from. _________________________________________________________________ [[alternative HTML version deleted]] </div

updated 17.2 years ago • Daren Tan

preformatted">It looks like there may be more than a 3UTR sequence for the same transcript that we identify through three keywords: hgnc_symbol, ensembl_gene_id, ensembl_transcript_id. It maybe caused by a bug in my script...such a weird situation real ? Thank you, Maura tutti i telefonini TIM! [[alternative HTML version deleted]] </div

updated 15.5 years ago • mauede@alice.it

Hi all, I am trying to identify genes that are specific to a cell type of interest by comparison with a large number of other cell types. To this end

deseq2 differential gene expression

updated 7.9 years ago • john.ouyang

Hi, guys! I was trying to install DESeq of Bioconductor 3.12 in Ubuntu under R4.0.4, but it didn't work. Moreover, I was told that package 'DESeq'is not available for this version of R. But what I'm confused is that I can install DESeq2 or other package of Bioconductor 3.12 successfully and I can't install DESeq under R4.0.3, either. Is any idea here? I really need your help.Thanks! ```r …

DESeq2

updated 4.8 years ago • Evy_00

biocLite.R", R calls for "http://bioconductor.org/biocLite.R" which explicitely checks for the R version and returns an error (R version should be above R.2.1.0). When taking a look at the biocLite.R script, this line caught...my eye: ## R versions less than 2.1.0 need to use the old (BioC 1.5) version of getBioC.R but I have no idea where to get the old version of getBioC.R

affy affy

updated 16.9 years ago • Leonor Palmeira

<div class="preformatted">Dear Bioconductor Subscriber, Just so you know that we released Custom CDF version 14 at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF _download.asp#v14 Our brainarray BioC repository is updated too. In this version, tiling chips are discontinued because of low usage, JCVIG and JCVIT cdf type is added for Medicago chip, an…

cdf cdf

updated 14.8 years ago • Manhong Dai