Bioconductor Forum

error message : error in getBM(c("structure_gene_stable_id", "structure_transcript_stable_id", : Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please...report. I have the following version of R on 64 bit : R version 2.8.1 RC (2008-12-20 r47269) Also, I have installed the release version and development version

GenomeGraphs GenomeGraphs

updated 17.0 years ago • Droit Arnaud

biomart = "ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org" ) #Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Entity 'nbsp' not defined Error: 1: Space required...after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Entity 'nbsp' not defined #[repeat 5 times with...mart) datasets…

software error biomart ensembl

updated 9.5 years ago • genomicsio

failed this is the wrong message and sessioninfo: > biocLite("AnnotationDbi") Running biocinstall version 2.0.8 with R version 2.5.0 Your version of R requires version 2.0 of Bioconductor. Warning message: package 'AnnotationDbi...in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > sessionInfo() R version 2.5.0 (2007-04-23) i686-pc-linux-gnu locale: LC_C…

Annotation annotate AnnBuilder AnnotationDbi Annotation annotate AnnBuilder AnnotationDbi

updated 18.6 years ago • lidaof

Hi I am comparing two different types of sequencing method for RNAseq. I am using the same set of samples (3 control, 3 treated) to prepare library using illumina mRNA kit and lexogen 3 prime library kit. The idea is to compare both library preparation method with the aim of using the three prime one for future experiments. we were hoping lexogen will generate roughly similar numbers of DGE, …

deseq2

updated 6.5 years ago • n.naharfancy

<div class="preformatted">Hi Any suggestions how to map gene symbols to mouse EntrezId(preffered) or Affy. mapping to Entez apparently is not supported by GSEABase > mapIdentifiers(gss,EntrezIdentifier()) Error in .mapIdentifiers_isMappable(from, to) : unable to map from 'Symbol' to 'EntrezId' neither GeneIdentifierType has annotation Error in GeneSetCollection(lapply(what, m…

updated 17.6 years ago • Vladimir Morozov

div class="preformatted">Hi guys, I tried to use SVA package to identify number of batch factors in my gene expression dataset. But I ran into an error message: > library(sva) > load("myeset.RData...Thanks a lot, Ying > traceback() 1: num.sv(edata, mod, method = "leek") > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) local…

sva sva

updated 12.4 years ago • Ying Chen

successfully generated a dseq2 from the count matrix but I want to add the respective chromosome numbers to the gene ids in deseq2 output. I am working with Oryza sativa. How to perform the annotation and with which annotation

NewWave hgu133a2.db

updated 2.3 years ago • roy23032

for example genes <-get.genes.by.pathway("path:hsa05416" ) works fine giving the list of gene identifiers. What could be the problem? Best regards, Tijana Marinkovic [[alternative HTML version deleted]] </div

updated 13.0 years ago • Marinkovic Tijana

the names, so why it doesn't work for assignment? This may or may not have something to do with the version of Limma... which leads me to my last question: Why does the development version of Limma get installed when using biocLite...haven't checked getBioC) I've seen that Gordon has said he doesn't keep "stable" and "developmental" versions like other maintainers and wants everyone to use the …

limma limma

updated 20.0 years ago • Jenny Drnevich

DE genes list. I have a couple of questions to ask, and hope someone can help me: Can I extract the number of genes, and IDs present in each enriched category using GOseq? If not, I suppose it is better to annotate all the genes

GO annotate Category goseq GO annotate Category goseq

updated 14.8 years ago • Biase, Fernando

and at the end of the analysis (so far) I am using the limma package (on linux/debian, most recent version of R). However, I am not able to find any DEGs. The problem is that these exact cel.files have been analysed before using...the Windows based software package provide by Affymetrix - and in that case several DEGs have been identified. So, something is not right but I do not really know wha…

R limma oligo differential gene expression affymetrix microarrays

updated 10.5 years ago • dennis.oezcelik

Hi Everyone, New user and first time posting to Bioconductor support page. I am also fairly new to R software Come up with a slight issue loading the 'rnaseqGene' package from this workflow http://www.bioconductor.org/help/workflows/rnaseqGene/\#abstract I am currently running the latest R version 3.4.4 for mac, however the 'rnaseqGene' package only seems to be compatible for 3.4.2 So my two…

rnaseq rnaseqgene R 3.4.2 Mac

updated 7.7 years ago • harry.horsnell.17

was not able to install the software.  Of course, the reviewer could have just installed a new version of R, but they incorrectly believed that v3.1 was the newest version available on OS X. Is there any way to make my package...available on older versions of Bioconductor?  Obviously, this is not ideal, but it is currently a barrier to publishing Thanks, - Gabriel&nbsp

bioconductor R software error biocinstaller

updated 9.6 years ago • gabriel.hoffman

<div class="preformatted">Hi Bioconductor users; I have a general question about limma model. In limma package, usually one linear model applies to all genes, and error variances from all genes are modified simultaneously. What if some factors, for example, one main effect, is only significant for some genes. Then if we want identify genes based on the significance of another main effect (o…

limma limma

updated 21.0 years ago • Fangxin Hong

<div class="preformatted"> Hi Weijun Luo, Using your two packages of gage and pathview, I have finished pathway analysis of signal transduction and identified two disturbed pathways from 40 pathways. But I met problem with metabolism pathway analysis, because I could not...your two packages of gage and pathview, I have finished pathway analysis of signal transduction and identified two dist…

Pathways gage pathview Pathways gage pathview

updated 12.1 years ago • Guest User

a new package on in the Developmental Packages section of www.bioconductor.org called RankProd. It identifies differentially expressed genes and estimates the associated percentage of false prediction (also known as...573 (2004) 83-92 It is a robust nonparametric method, which would gain power in the case of low number of replications and/or relatively large scale of noise. The method can natu…

RankProd RankProd

updated 20.8 years ago • Fangxin Hong

Me-DNA is hybridized to Affymetrix human promoter 1 array. I am using shirley Liu's MAT for identifying the peaks. I got around 7K peaks of which I selected peaks with FDR with 2%. The number of probes is 3K. I am using Galaxy

updated 16.8 years ago • Adrian Johnson

Hi, I am very new to DESEQ2 and I am struggling to create the initial Deseq2 dataset. I have a zip file with HT-seq counts for 5 days and each has a certain number of repeats, there are 22 files in total in the zip file. Each with the counts from each studied day. I don't understand how to get this into a format to where I can do differential analysis across all days to find out which day a cert…

DESeq2 timepoints

updated 4.8 years ago • Chloe

I have to delet the item to get the command to work, and this causes results to be returned absent identifiers. I'm referring to the following command: toptable(coef=2,number=15,genelist=genelist[,1:6],fit=fit,eb=eb,adjust ="fdr

limma limma

updated 21.8 years ago • Dennis Hazelett

Now that the version of R no longer determines the version of BioConductor, I need to change my definition and approach to staying "current...Now that the version of R no longer determines the version of BioConductor, I need to change my definition and approach to staying "current" with my institute-wide installation of R and attendant libraries, especially BioConductor.  I used to promi…

version release library

updated 10.8 years ago • Malcolm Cook

Hi all, I was wondering if there is anyway to get ChIPpeakAnno to report the total number of covered bases (as opposed to the number of overlapping regions) when making use of makeVennDiagram()?  Is this

chippeakanno

updated 10.9 years ago • Brad Davis

already been answered. I have been using CellHTS2 for a while now but have recently upgraded to R version 2.9.1 and CellHTS2 version 2.8.1. Using my previous version I could miss replicates from the plate list file without...differing number of rows: 3, 2 . I have tried it also when missing replicate 2 and replicate 3 and I still get the error. Can I still analyse...with a different number of…

Cancer cellHTS2 Cancer cellHTS2

updated 16.4 years ago • Becky Saunders

below as well). Am I missing something, or is there a problem somewhere in the developmental version or in a dependent package? Let me know if you need more info... Thanks, Jenny > sessionInfo() R version 2.6.0 Under development...not attached): [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-21 > sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: L…

GO Survival hgu95av2 annotate affy affydata graph Rgraphviz limma gcrma matchprobes GO

updated 18.3 years ago • Jenny Drnevich

I do, when I run `normalize(filtered.sce)`, I get the error: `size factors should be positive real numbers`. It is my understanding that even though `computeSumFactors()` coerces to positive by default if necessary, it doesn...lt;- normalize(filtered.sce)` - Error in .local(object,...): size factors should be positive real numbers I even tried filtering by `keep <- ave.raw.counts &…

scater scran singlecellexperiment normalize qc

updated 6.6 years ago • kushshah

the clustering results. When I upgraded the R software on my local machine, I have installed latest version of hopach package "version 1.4.3". In this latest version, the makeoutput() function is removed. Is there are any other...improvised function that has replaced makeoutput() function in the latest release of he version 1.4.3 ? . As I have already saved the code for the makeoutput() function…

Microarray Clustering hopach Microarray Clustering hopach

updated 17.6 years ago • Suprabhath Reddy

When can we expect the latest versions to be available on bioconductor and bioconda? I am particularly interested to use the "dtuScaleTPM" method... Cheers

tximport

updated 7.4 years ago • sebio

of traceback()? >>> >>> This would happen if, for example, oligo finds the old version of >>> the >>> pd.mapping250k.sty package. >>> >>> b >>> >>> On Jun 4, 2007, at 8:07 AM, De Bondt, An...wrote: >>> >…

SNP oligo SNP oligo

updated 18.6 years ago • Benilton Carvalho

annotation package for a platform that has a single human assay. The platform currently has older versions of the assay, and data obtained from those older versions are still in use (but no longer being produced). For example...let's say Platform X can run a single assay, Assay Y, and a new version of Assay Y is released every couple of years. The newest version is v5.0, and the previous version …

ChipDb AnnotationDbi AnnotationForge

updated 3.0 years ago • ahiser

In my PureCN results I see with most samples that there will be long stretches of the genome, e.g. many separate chromosomes, where the copy ratio (2 ^ log ratio) is approximately but not exactly 1, such as for example 1.02, 1.03, 0.98.  Typically the number is consistent in any given sample, perhaps differing by no more than 0.01.  When I try to get a p-value for whether or...I…

PureCN CopyRatio

updated 7.2 years ago • twtoal

and control is 425. In the second matrix, cases are 11 and control is 16. The differences in the number of genes is due to filtering of genes with zero row sums. The design matrix is set up to identify DE genes in control (1) vs...I have been trying to attribute this altered logFC in both datasets to either the differences in the number of samples and the groups being imbalanced with greater…

Transcriptomics edgeR DEG

updated 7 months ago • Maziya

<div class="preformatted">Dear Jan, The first step is to read the documentation! Page 9 of the edgeR User's Guide says: "If the counts for different samples are stored in separate files, then the files have to be read separately and collated together. The edgeR function readDGE is provided to do this. Files need to contain two columns, one for the counts and one for a gene identifier. …

Normalization edgeR Normalization edgeR

updated 12.6 years ago • Gordon Smyth

for finding overrepresentation pathways. For example, the high abundance proteins were easier to be identified in a proteomics experiment because of the limitation of current analysis method. If all of the proteins for the...changed proteins, the pathways with high abundance proteins would be found. So I think the proteins identified in this experiment is better reference than all of the proteins…

Proteomics Pathways KEGGprofile Proteomics Pathways KEGGprofile

updated 13.0 years ago • slzhao

r > BiocManager::install("Bioconductor") Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15 ucrt) Installing package(s) 'Bioconductor' Warning message: package ‘Bioconductor...is not available for Bioconductor version '3.16

Bioconductor Install

updated 2.7 years ago • 3305504122

Please help,   package ‘virtualArray’ is not available (for R version 3.2.1)   Should I wait? When it will be available?   Thank you! &nbsp

r update

updated 10.5 years ago • filip.roudnicky

div class="preformatted">Is there a function to determine which version of R you are running? For example, quartz() will work on Macs, but not on Windows. Thanks! Simon </div

updated 19.3 years ago • Simon Lin

to see if It works. Sorry...*** Hi, I'm working on a SNP analysis project where the goal is to identify common/different polymorphism between groups of samples. The VCF files I am using contains multiple samples with...3 position on a given chromosome with different genotypes ##fileformat=VCFv4.2 ##INFO= <id=dp,number=1,type=integer,description="approximate depth"="" read=""> #…

VCF VariantAnnotation

updated 19 months ago • Marco

Hi all, I am trying to create an ExpressionSet from scRNAseq data so I can identify cell-type composition using the MuSiC Deconvolution method, however, the last line of the code gives an error like...that: > Error in validObject(.Object) : invalid class “ExpressionSet” object: > 1: sample numbers differ between assayData and phenoData invalid class > “ExpressionSet” object…

deconvolution r scRNAseq bioinformatics

updated 3.9 years ago • alanya.hasan

<div class="preformatted">Hi, ----> Thanks for your response regarding mapping IMAGE clone IDs to unigene. I have some further questions I am not using Affymetrix arrays. This is why I don't think that downloading the "Annotation CSV" files will help me? It seems that in the examples on the vignettes that the starting point is a list containing Affymetrix probe id's and then Genba…

Microarray GO probe AnnBuilder Microarray GO probe AnnBuilder

updated 22.1 years ago • Law, Annie

BiocInstaller to install S4 vectors, it installs 0.20.1 I think I'm lost on how to connect the versions and force BiocInstaller to get the version of tool I'm interested it. `BiocInstaller_1.32.1 tools_3.5.0 BiocManager_1.30.10...I'm unsure if these versions are in line with R3.5. Any pointers here in order to achieve the desired goal shall be highly appreciated

software error installation

updated 6.0 years ago • GENOMIC_region

Hi, I recently got the new version of ChAMP 2.8.9 and now I can not proceed through champ.DMP, an error now occures that did not show up when I was using...the previous version 2.8.7. champ.DMP runs without problem until the annotation section. <pre> myDMP <- champ.DMP(arraytype = "EPIC") #now it...in my samples/sample sheet was changed. Any idea what might be the problem? Could…

champ

updated 8.4 years ago • sarka.vorackova

div class="preformatted"> Dear All, I updated my annotation library lumiHumanAll.db into version 1.10.1 but I'm unable to load it correctly. The error message is below. The latest version is created with R-version 2.11.1...has updated dbconn. Is there any way I could downgrade both dbconn and lumiHumanAll?? Can the old versions be found somewhere?? Loading required package: org.Hs.eg.db Err…

Annotation Annotation

updated 15.3 years ago • Mervi Alanne

<div class="preformatted">Hi, I would like to use the latest development KEGG.db for something. DOes anyone know how to install it? I would really like just that one package, but can cope with the development version if necessary. It would just save some work converting from old KEGG IDs to new. Dan -- ************************************************************** Daniel Brewer, Ph.D. …

Cancer Cancer

updated 16.7 years ago • Daniel Brewer

DESeqDataSetFromMatrix use to work in R-3.1.2. with DESeq2 downloded from biocLite. Now with newer version R and DESeq2, I got the following error. Could anyone help me? It could be I need a different version of DESeq2. Here is the

DESeq2

updated 3.9 years ago • pam

inputAnnotation=FALSE) > raw Summary of BeadStudio output: Illumina Inc. BeadStudio version 3.2.6 Normalization = none Array Content = mouseMI_V1_R0.bgx.xml Error Model = none DateTime = 03/03/2008 16:39 Local...5240 (386 total) fvarLabels and fvarMetadata description: TargetID: The Illumina microarray identifier experimentData…

Microarray Normalization lumi BRAIN Microarray Normalization lumi BRAIN

updated 17.7 years ago • Cei Abreu-Goodger

Teen Patti Star customer care helpline number ✅ 7908285003 call now

cellxgenedp

updated 2.6 years ago • Customer

Dear BioConductor Community, I am using the UniProt.ws version 2.10.2 to retrieve features for my protein hitlists. I am particularly interested in the SUBCELLULAR LOCATION...Dear BioConductor Community, I am using the UniProt.ws version 2.10.2 to retrieve features for my protein hitlists. I am particularly interested in the SUBCELLULAR LOCATION information

uniprot.ws subcellular location uniprot

updated 9.9 years ago • DHS

div class="preformatted">Hello, How can I install previous version of DEXSeq (1.6.0)? -- output of sessionInfo(): .. -- Sent via the guest posting facility at bioconductor.org. </div

DEXSeq DEXSeq

updated 11.6 years ago • Guest User

trying to map SNPs to the nearest genes. We find we're getting different mappings depending on the version of GenomicRanges used, even when the input files are the same. I've pasted our code below. I looked at 3 of the discrepant...the UCSC genome browser (to visually confirm which gene was infact closer). It seemed to me that one version mapped the SNP to the nearest gene and the other seemed to…

GenomicRanges distancetonearest strandedness

updated 7.7 years ago • shraddha.pai

<div class="preformatted">Hello, I am interested in accessing old versions of GO.db and org.Hs.eg.db data. I would like to them to potentially be different versions, so entirely downgrading bioconductor and/or R (the standard response) does not seem to make sense. Also, I recognize that identifiers and mappings may be missing or not match -- That is ok. After reading through the Annotatio…

Annotation GO AnnotationDbi Annotation GO AnnotationDbi

updated 11.6 years ago • Guest User

for details replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) 'destiny' Warning message: In .inet_warning(msg) : package...destiny’ is not available for Bioconductor version '3.13' A version of this package for your version of R might be available elsewhere, see the ideas at h…

destiny BiocVersion

updated 4.5 years ago • Yiming

I want to identify differentially methylated probes(DMPs) between two groups.  After preprocessed raw data, 666805 probes remained...Probes with BH adjusted P value<0.05 were considered as DMPs. As a result, 134841 probes were identified as DMPs. It reveals nearly 1/5 probes was differentially methylated between our two groups. btw :the chip we used...using IMA. I compared those…

limma methylation methyanalysis IMA

updated 8.8 years ago • RC

I'm looking at identifying differentially expressed genes. I'm using Salmon, importing the quantification using tximport as outlined...one rep is unfortunately a bit different from the other (actual gene expression). As a result, the number of DE genes is reduced and is making any biological interpretations challenging. To help with this, I'd like to use RUVSeq

Salmon DESeq2 DEG RUVSeq

updated 4.5 years ago • reganhayward

Hi, I'm new to this so apologies if my question is very simple.... I conducted DESeq2 anlaysis for some 16S rRNA sequencing data. I compared the differentially expressed genes between two time points. Example results for one OTU is below, so a log2 fold increase of 24.2 from timepoint 1 to 2. Please can someone explain what this actually means? And also what the base mean is? My sup…

deseq2

updated 6.8 years ago • tegan.sutton

5\] "gi|118130860|ref|NM\_133839.2|" "gi|29789242|ref|NM\_024451.1|" I thought that the numbers following 'gi|' would be entrez gene identifiers.  So I tried org.Mm.eg.db. But this doesn't seem to work: > x <- org.Mm.egGENENAME

annotation

updated 8.2 years ago • Ed Siefker

Dear Bioconductor support team, I have samples from two time points namely __V1 and V4__. The samples belong to two categories: Treatment and Placebo as follows: 005v1 Placebo 005v4 Placebo 008v1 Treatment 008v4 Treatment The ID number 005 etc represent the __same sample at two time__ points. At V1 time-point there is no treatment given, its just that the...follows: …

edger limma paired design

updated 7.0 years ago • candida.vaz

<div class="preformatted">Good afternoon! I hope this question is not redundant - I've tried searching the mailing list archives and doing a Google search. I've just finished using aroma.affymetrix() to produce allele-specific copy number estimates. So, right now, I've got the allele frequency data, i.e. what the vignettes call "fracB" data. I would like to run circular...doing a Google s…

aCGH aCGH aCGH aCGH

updated 15.4 years ago • Christine Ho

expression levels are indeed comparable between species. What I did so far: - Used orthoMCL to identify single copy orthologous genes - Generated a matrix with raw counts of all single copy orthologous genes for each...might be an issue since the model doesn't know that there is quite some variation in genome size and number of genes between the species, and it doesn't know the sequencing …

deseq2 wgcna

updated 8.6 years ago • jcfnielsen

<div class="preformatted">Hi, Which libSBML version is required for rsbml? I couldn't find this information anywhere, and it doesn't work for libSBML 3.4.1 (and 2.4.0) on Fedora...div class="preformatted">Hi, Which libSBML version is required for rsbml? I couldn't find this information anywhere, and it doesn't work for libSBML 3.4.1 (and 2.4.0) on

updated 15.9 years ago • Rainer Machne

packages/3.1/bioc")' Warning message: package ‘BiocInstaller’ is not available (for R version 3.2.2) > tried with this step also : (install.packages("BiocInstaller", repos="http://www.bioconductor.org/packages

biocinstaller

updated 10.4 years ago • anikumar.murugan

m <- as.matrix(RG) d <- DGEList(counts=m, group=(1:2)) #modify 'group' depending on sample number. Also can be adapted to replicated samples, see'?DGEList'. d et <- exactTest(d, pair=(1:2),dispersion=bcv^2) #exactTest(RG, pair...Check the individual cpm values for the top genes: summary(de <- decideTestsDGE(et)) #The total number of DE genes at 5% FDR is given by'd…

edgeR edgeR

updated 12.2 years ago • biotech