Bioconductor Forum

u133plus2 array and interested in classification disease/control using microarray data. We have identified a molecular signature and trained a svm-based classification model based on 200 samples (100 disease +100 control...sender immediately and delete this message, along with any attachments. [[alternative HTML version deleted]] </div

Microarray Classification PROcess Microarray Classification PROcess

updated 16.1 years ago • qinghua.XU@as.biomerieux.com

normalization + summarization (target = core) using the bioconductor package oligo (bioconductor version 3.7.). When using the bioconductor package pd.hugene.2.1.st, 38598 out of 53617 features have a valid geneassignment...package hugene21sttranscriptcluster.db x<-hugene21sttranscriptclusterENTREZID #get the probe identifiers that are mapped to an Entrez Gene ID mapped_probes<-m…

annotation microarray bioconductor pd.hugene.2.1.st hugene21sttranscriptcluster.db

updated 7.2 years ago • Irene

fix that you kindly provide has been included in the updated development (1.7.5) and release (1.6.2) versions of the GSVA package. thanks again for bug reporting, and this time, even fixing!! :) robert. On 01/16/2013 11:55 AM, Luca Beltrame...GSVA/R/gsva.R 2013-01-16 11:19:36.518699558 +0100 @@ -123,7 +123,7 @@ cat("Mapping identifiers between gene sets and feature names\n") …

Annotation GSVA Annotation GSVA

updated 12.9 years ago • Robert Castelo

<div class="preformatted">Hi Folks, I want to run a GSVA analysis on a set of Affymetrix hgu133plus2 arrays. To familiarise myself with the GSVA code, I worked through the example in the vignette, but encountered the following issue... > data(leukemia) > data(c2BroadSets) > library(parallel) > filtered_eset <- nsFilter(leukemia_eset, require.entrez=TRUE,…

PROcess GSVA PROcess GSVA

updated 12.9 years ago • David Iles

among samples. The authors of this paper then used The differentially expressed transcripts were identified using M-A based random sampling method implemented in DEGseq package in BioConductor ( http://bioconductor.org...some time in learning the bioconductor program! Many thanks JILL [[alternative HTML version deleted]] </div

Transcription DEGseq Transcription DEGseq

updated 13.2 years ago • Jill Pleasance

cellHTS objects separately via the 'raw', 'normalized' and 'scored' arguments` As I cannot identify the source of the error, I am not sure what it means or which files / commands I will have to change. Do you have any experience...alternative HTML version deleted]] </mailto:regina.hecker@kispi.uzh.ch></div

cellHTS cellHTS

updated 16.5 years ago • Hecker Regina

Added genomeRNAi filters and attributes for Human and Fruitfly. An example identifier has been added for all the RNAseq attributes. Ensembl Variation 70: Updated the human somatic variation database...EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK [[alternative HTML version deleted]] </div

genomes genomes

updated 12.9 years ago • Thomas Maurel

gpr" [1] "Reading ....gpr" [1] "Reading ....gpr" [1] "Reading ....gpr" Warning messages: 1: number of rows of result is not a multiple of vector length (arg 2) in: cbind(Gf, as.numeric(dat[[name.Gf]])) 2: number of rows of result...is not a multiple of vector length (arg 2) in: cbind(Gb, as.numeric(dat[[name.Gb]])) 3: number of rows of result is not a multiple of vector lengt…

updated 22.5 years ago • White, Charles E WRAIR-Wash DC

to get metaXCMS working it didn't succeed. The problem is loading of a mzR ? There is a different version of Rcpp ? I hope someone can help me with this problem ? Thank you already for your help. Best, Wishes, Siebolt. > library...setDummyField' not found In addition: Warning messages: 1: package ???Rcpp??? was built under R version 3.0.1 2: In fun(libname, pkgname) : mzR has been bui…

mzR mzR

updated 12.2 years ago • Guest User

Error in checkForExperimentalReplicates(object, modelMatrix) : The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as replicates was...deprecated in v1.20 and no longer supported since v1.22. ``` Not sure if it's a version issue and downgrading DESeq2 will fix it or if there is a more serious issu…

DESeq2 scRNAseq

updated 3 months ago • rj1435

This technically pertains to the command line featureCounts program in subread, but the subread webpage suggests posting here, and I'm assuming the bioconductor version has the same functionality. I'm trying to count only fragments that span splice junctions (per gene as the meta feature) in featureCounts using the --splitOnly option. The documentation suggests that this will capture reads wit…

Rsubread

updated 2.2 years ago • Gregory

Hi, I am running the generic version of enricher supplying my own GO mappings. When I create a dotplot from this object, I get a dotplot with less genes than...DEGs from DESeq2 and go_mappings are the gene and respective GO term that I'm supplying. My total number of DEGs is about 500, and the dotplot shows about 100 if I add up all the categories. (Is there a way to include my image?) …

clusterProfiler enrichplot

updated 3.5 years ago • Lucía

and up to 34TB swap. I know from R FAQ that "There are also limits on individual objects. On all versions of R, the maximum length (number of elements) of a vector is 2^31 - 1 ~ 2*10^9" But: 2.147.483.648 = 2^31 is bigger than 1.770.343.000

hgu133a hgu133a

updated 18.8 years ago • Ivan Porro

KOcontrol) fit=lmFit(MA,design) fit=eBayes(fit) option(digits=3) result=topTable(fit, coef=2, number=6384, adjust="BH") as.matrix(result) write.csv(result,file="printtiploess.csv", quote=FALSE, col.names=TRUE, sep=",") Regards...S. Fazeli MSc Student of Chem. Eng. ferdowsi University mashhad Iran* [[alternative HTML version deleted]] </div

limma PROcess limma PROcess

updated 14.6 years ago • samane fazeli

the goseq db for Mycoplasma hyorhinis.  Here is what I used: makeOrgPackageFromNCBI(version = "0.0.1", author = "me", maintainer = "me <me@mine.org>", outputDir = ".", tax\_id = "1129369", genus = "Mycoplasma", species = "hyorhinis", NCBIFilesDir...a method for function 'unique': Error in .Method(..., deparse.level = deparse.level) :    …

AnnotationForge

updated 10.0 years ago • songeric1107

after approximately 15 minutes. Am I doing something wrong or is there an upper limit for the number of regions in a biomart query? Thanks in advance, Christian > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-pc-linux

biomaRt biomaRt

updated 15.4 years ago • Christian Ruckert

Mycoplasma", species = "hyorhinis", but I get error, could you please help. makeOrgPackageFromNCBI(version = "0.0.1", author = "me", maintainer = "me <me@mine.org>", outputDir = ".", tax\_id = "1129369", genus = "Mycoplasma", species = "hyorhinis", NCBIFilesDir...a method for function 'unique': Error in .Method(..., deparse.level = deparse.level) :    number of c…

go

updated 10.0 years ago • songeric1107

How can we cope with the many uncontrollable factors and be able to use 80 , 200 or even a higher number of arrays at the same analysis fixing for any of the uncontrollable effects. I am using mostly Affymetrix arrays , Hu133plus2...incorporates. Thanks in advance. T. Paparountas www.bioinformatics.gr [[alternative HTML version deleted]] </div

GeneSpring GeneSpring

updated 16.8 years ago • Paparountas Triantafyllos

the tx2gene data.frame is to use the ensembldb packages. The annotation packages can be found by version number, and use the pattern EnsDb.Hsapiens.vXX. _ The exemple is for human data. My question is: how to do in bovine

tximport ensembldb bos taurus tx2gene

updated 7.4 years ago • gilles.charpigny

using C-difficile two-color microarrays and would like to do some pathway analysis. KEGG has quite a number of pathways for this organism (see http://www.genome.jp/kegg- bin/show_organism?menu_type=pathway_maps&org=cdf...but when I tried to access them with KEGG.db (version 2.4.5, R 2.12.0) I had no success, e.g. if I type "KEGGPATHID2EXTID$hsa00010" I do get a list of genes present in th…

Organism Organism

updated 14.7 years ago • Claus Mayer

data using rma function of affy library I can see the names of the samples as they were and sample numbers namely 1,2,3,4. What I understand is it takes alll the four samples as different and when I do the differential expression...to proceed Any help will be much appreciated. Thanks , Himanshu Sharma. [[alternative HTML version deleted]] </div

affy limma affy limma

updated 13.7 years ago • hsharm03@students.poly.edu

d) gives 0.0005329. So I am wondering if I could use 0.0005329 since I have rather big number of samples in each group. Or I should adjust prior.n into 10 according to the manual's suggestion. 2. TMM I am not sure if...package and hope you may give some suggestions. Many thanks! Ying Ye [[alternative HTML version deleted]] </div

Normalization edgeR Normalization edgeR

updated 15.2 years ago • Ying Ye

was thinking that they should be equivalent due to (D - A) - (C - A) = D - C, but I obtain different numbers of significant DE Genes from these two methods so it seems like my thinking is incorrect. I am using DESeq2 version

deseq2 comparison of comparisons compare two contrasts complex contrast

updated 6.7 years ago • dbretta25

plot. I was thinking about doing it by subtracting each of the posions over 2.1M with the fitted number so that it will end on the other side at the right position (e.g. subtract 6.3M from position 4.2M, so that I will get position...Is there an easier way of doing it? thanks in advance for he help Assa [[alternative HTML version deleted]] </div

updated 11.8 years ago • Assa Yeroslaviz

use the weights. Many thanks in advance for any suggestions! Cheers, al > sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252...Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 27429…

Survival annotate genefilter limma Survival annotate genefilter limma

updated 18.5 years ago • Al Ivens

Sample", 1:5) # Error in `sampleNames<-`(`*tmp*`, value = c("Sample1", "Sample2", "Sample3", : # number of new names (5) should equal number of rows in AnnotatedDataFrame (3) Alternatively, I could change the rownames of raw1...am just curious as to why this error message. Thank you. Regards, Adai [[alternative HTML version deleted]] </div

beadarray

updated 11.3 years ago • Adaikalavan Ramasamy

Dear all, I used AnnBuilder to annotate a customed array. One of gene is pla2g2a, its Access number is NM_011108, its ID number in my array is 4842. however I could not get its symbol from the annotation package I made, neither...baseMapType = myBaseType, pkgName = "custommice", pkgPath = myDir, organism = "Mus musculus", version = "1.2.0", author = list(authors = "Yihuan Xu", maintainer = "Yih…

Organism annotate AnnBuilder Organism annotate AnnBuilder

updated 18.2 years ago • Yihuan Xu

Error in .local(object, ...) : subscript out of bounds This is my session info sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF...raw data AffyBatch object size of arrays=1050x1050 features (21 kb) cdf=exon.pmcdf (1411189 affyids) number of samples=12 number of genes=1411189 annotatio…

Normalization cdf exonmap Normalization cdf exonmap

updated 14.7 years ago • Gomez Moruno, Antonio

wrong there, is not the problem though - my GT and DP feilds are present: ##FORMAT= <id=gt,number=1,type=string,description="genotype"> ##FORMAT=<id=dp,number=1,type=integer,description="approximate (reads="" are="" bad="" depth...see is the PL field where is says the number is G, rather than 0 or 1. I presume this is correct as I haven't been able to find any specification …

variantAnnotation

updated 6.2 years ago • b.curran

nbsp;             Uniquely mapped reads number |       31138446                &nbsp...nbsp;&am…

featurecounts bioconductor differential gene expression star

updated 8.9 years ago • gregory.l.stone

Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London...NW1 2BE. > > > > [[alternative HTML version deleted]] > > __________________________________________…

SNP IRanges SNP IRanges

updated 11.7 years ago • Vince S. Buffalo

lt;<<< ChAMP.FILTER START >>>>>] ----------------------------- ``` In New version ChAMP, champ.filter() function has been set to do filtering on the result of champ.import(). You can use champ.import...Filtering probes with a detection p-value above 0.01. Removing 2728 probes. If a large number of probes have been removed, ChAMP sugg…

pipeline testdata ChAMP

updated 3.0 years ago • luisfranciscoteves

Hi everyone, Is there any script that links DE genes identified by DEseq2  directly to ReactomePA for Functional enrichment analysis? thanks much &nbsp

ReactomePA GO

updated 9.2 years ago • ta_awwad

Files.I have performed normalisation,preprocessing using R Package and when i am proceeding in identifying differentialy expressed genes,i am getting all adjusted p-values in range of 0.99.How to proceed with it

differential gene expression

updated 10.9 years ago • priyadharsh222

I would like to be able to identify samples where the gating applied with opencyto is odd. Instead of inspecting each sample, I am thinking of plotting

opencyto

updated 9.6 years ago • Ulrik Stervbo

didn't know where to start with finding a solution. I've included my code below (note that the low number of AS bins is normal for this genome, as there are very few annotated AS events.) I would greatly appreciate any help with...the 'metadata' data frame ... OK Make the TxDb object ... OK > features <-binGenome(TxDb) * Number of extracted Genes = 5712 * Number of extracted Ex…

ASpli

updated 4.6 years ago • Emma

in the nrmData function. Is this the way to do? Thanks for your help! >sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE...Helsinki Department of Forest Sciences Latokartanonkaari 7 PO Box 27 00014 Helsinki (Finland) Phone number: +358 504486086 email: tommaso.raffaello@helsinki.fi email: t…

qPCR EasyqpcR qPCR EasyqpcR

updated 11.5 years ago • Tommaso Raffaello

<div class="preformatted">Dear Gordon, I am working with a set of illumina microarray data (96 samples) from three groups (i.e. group-1(X),group-2(Y),group-3(Z)). 32 samples from each group. I have read the data using lumiR method and processed the data using lumi Methods(lumiExpresso). Now I need to identify the differentially expressed genes by comparing each of these groups with each …

Microarray limma Microarray limma

updated 16.3 years ago • Md.Mamunur Rashid

I have a list of regions identified as differentially methylated regions using bump hunter in minfi package with the format <span style="line-height...end ….</span> `` chr1 `` `` chr2 `` `` chr3 `` `` …. `` <span style="line-height:1.6">I want to identify genomic features of these positions (5' UTR, exon, gene body or 3' UTR)</span> <span style="line-height:1.6">…

genomicfeatures

updated 9.3 years ago • Asma rabe

best hit using blastp for a long list of proteins for which I'm given only the UniProtKB/TrEMBL identifier. I have to find the ortholog proteins for each of the given proteins. I also have to find orthologs in a given list...when I had only one Protein, I would do it through online tool in NCBI, there I can give the identifier and also limit the species. However, with more proteins in hand, this …

blast R

updated 9.9 years ago • maahpishanu

as the rownames. The featureData slot is empty, and hence I just have a sequential rownumber as the identifier instead. I tried an upgrade to the dev version but the probeIDs were also not attached. How can I fix this? Command...X1814671034_D.AVG_Signal, X1814671034_E.AVG_Signal > sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_New Zealand.1252;LC_CT…

updated 17.9 years ago • Johnstone, Alice

Hi! I have a question that I have been asking myself for a long time and after reading different forums on best approaches to take bath effects into consideration in the analysis workflow, I am still left perplexed. I have two different datasets from my own lab: 1) mRNAseq datasets which come from after purification of mRNA from captured polysome fractions followed by sequencing . I did polyn…

DESeq2

updated 22 months ago • Kuldeep

file ... Importing as <hugene-1_1-st-v1.cxy>... <803480> records imported...Finished Warning: Number of entries <803480> is not equal to <1178100>. New dataset <hugene-1_1-st-v1> is added to Content... Importing as <hugene...1_1-st-v1.anp>... Number of probesets is <257430>. <33297> records read...Finished &…

Microarray xps Microarray xps

updated 13.2 years ago • Juan Fernández Tajes

I can read it from my pc machine. > >The verion of R on supercomputer is 1.7 and the version of R on my pc >machine is 1.9. > >How can I solve this problem???? > >Thanks > >pingzhao > >_______________________________________________

cdf affy cdf affy

updated 21.3 years ago • Joyce Gu

my Bam files using TEQC package which have been aligned on a reference with the following format chr number (1-19, X, Y ), start (integrer), end (integrer) the chromosomes are not with the prefixe chr. When I try to create the target file...the only way to change everything back to chr prefixes???? many thanks Nat > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-l…

Coverage Coverage

updated 13.5 years ago • nac

<div class="preformatted">Dear Laura, Here is a reproducible example of edgeR code for finding genes that are DE between any of your cultivars, regardless of which cultivars: nlibs <- 24 cultivar <- factor(c(1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12)) design <- model.matrix(~cultivar) y <- matrix(rnbinom(ngenes*nlibs,mu=50,size=10),ngenes,nlibs) d &…

edgeR baySeq edgeR baySeq

updated 14.1 years ago • Gordon Smyth

profileCGH) 4: BkpInfo(profileCGH) - OS: Debian GNU/Linux, a mixture of testing and unstable - version of gcc/g++: 4.8.2-1 and 4.7.3-9 (for Debian) - version of GLAD: 2.26.0 (for R-3.0.2) and 2.27.1 (for R-3.1.0) - versions of R: several...from R-3.0.2 and R-3.1.0. For instance ## the current Debian version > version _ platform x86_64-pc-linux-gnu arch …

GLAD GLAD

updated 12.0 years ago • Ramon Diaz-Uriarte

clear: The $MergedPeaks from FindOverlappingPeaks and MakeVennDriagrams actually give out the same number of peaks. The problem is that in the venn diagram itself a smaller number of peaks is shown as overlapping both datasets...Npeaks1 + Npeaks2), useFeature=FALSE, minoverlap = 100, > select= "first") > > and the number of peaks ($MergedPeaks) from: > findOverlappingP…

Genetics GO ChIPpeakAnno Genetics GO ChIPpeakAnno

updated 13.2 years ago • Julie Zhu

div class="preformatted">Hi Lauro -- This was a change in the development version of R over the weekend (r32748, 2007-09-04 02:33:30 -0700, I think) and was fixed in the development version of Biobase the same...http://bioconductor.org/biocLite.R') > biocLite('Biobase') As you found out, using development versions of R and Biobase can have very unfortunate consequences. When offering …

Microarray Biobase Microarray Biobase

updated 18.3 years ago • Martin Morgan

type 2. Detection method 3. PubMed Id of article documenting the interaction 4. Many alternate identifiers, with protein identifiers dominating An IDMapper class provides HUGO gene symbols for most of the several kinds...of protein identifiers returned by PSICQUIC.   RefNet currently adds a human metabolic network (recon2), stamlab TFs, and a 2006 angiogenesis

shiny network interactions

updated 11.1 years ago • pshannon

div class="preformatted"> Hello, Short summary version: How to interpolate a micro-array time series to get differentially expressed genes at a time point that was not measured...Long version: I'm analyzing a two species (human and mouse) and two groups (control and treatment) time series (9 time points) micro-array...As an example I have a 48h sample for human, and 42h and 50h samples for mou…

limma limma

updated 11.8 years ago • Guest User

different samples) and now want to compare the modules. But, I'm running into this error with R version 4.0.0. I had the same error when importing the RData of module colors from previous network analyses: ```r # Expression...colorList, referenceNetworks = c(1:2), : Color vector for set 1 does not have the correct number of entries. Timing stopped at: 0.033 0.008 0.04

preservation WGCNA

updated 4.0 years ago • Sara

<div class="preformatted">Hi There, I am a newbie to Bioconductor. I am trying to get off the ground with regards to my analysis. My question is as follows. 1) I have a list of 1000-2000 SNP's which are associated with a set of few diseases (Hemochromatosis etc). 2) We would like to use Affy6.0 Chip to look for the presence of these SNPs experimentally. 3) Even before we use the chips, H…

GLAD GLAD

updated 14.9 years ago • quantrum75

without any manipulation. I checked the code of readCodelink, it seems there should be product, number of genes..... fields. Would you like to help me about this? Will the file needs more header to be recognized by the codelink...package? Thanks a lot, Lixia [[alternative HTML version deleted]] </div

codelink codelink

updated 17.3 years ago • Diao,Lixia

pamr.listgenes(NSC.trained, data, threshold=optthresh, genenames=TRUE) However, if the total number of genes at the opt. threshold is only one the following error mssg. is obtained: Error in dimnames(res) <- list(NULL, c("id...and Bioinformatics School of Information Technology JNU New Delhi [[alternative HTML version deleted]] </div

pamr pamr

updated 17.3 years ago • ALok

I'm running PureCN (developer version 1.11.8) on a new project, and a number of errors occur, one of which is: <pre> INFO [2018-06-20 13:46:48] Done. INFO [2018-06-20 13:46

PureCN

updated 7.3 years ago • twtoal

GeneColorSet" object: gene and color lengths differ It seems that there is a problem when the number of genes/probes in the set changes. Regards, Hans-Ulrich > sessionInfo() R version 2.6.2 (2008-02-08) x86_64-pc-linux-gnu

updated 17.7 years ago • Hans-Ulrich Klein

param = cwp)</pre> <pre> xod <- adjustRtime(xod, param = ObiwarpParam())</pre> <pre> Sample number 6 used as center sample. Aligning SJ45.CDF against SJ50.CDF ... Error: BiocParallel errors element index: 1, 2, 3, 4, 5, 6, ... first...of adjustRtime it all works, but I'd really like to try the new functions! Any insights? <pre> R version 3.4.0…

xcms obiwarp adjustrtime metabolomics

updated 8.1 years ago • bhgyu

6] "IntT8vsT2" "IntT24vsT8" >KW_0h <- topTable(fit2, coef="KW.T0", sort.by="P", adjust='fdr', number=nrow(sig.norm)) >KW_2h <- topTable(fit2, coef="KW.T2", sort.by="P", adjust='fdr', number=nrow(sig.norm)) >KW_8h <- topTable(fit2...coef="KW.T8", sort.by="P", adjust='fdr', number=nrow(sig.norm)) >KW_24h <- topTable(fit2, coef="KW.T24", sort…

updated 12.6 years ago • Natasha

This is ~100000 short of what is needed for 1 affinity per probepair but if you divide it by the number of arrays I had = 159683/7 = 22811.86 it is pretty close to the number of probesets on the array(22810). So this would imply...gt; sessionInfo()) R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "da…

ath1121501 cdf probe Biobase affy plier ath1121501 cdf probe Biobase affy plier

updated 20.2 years ago • Matthew Hannah