Bioconductor Forum

<div class="preformatted">Dear List, I have another question with the xps package. I installed root and xps, created the root schemes for the HuGene1.0 array and imported the first CEL files following the example scripts. Everything works fine to that point. However, after RMA normalization I'm missing a couple of probesets. When I use the Affymetrix expression console you get 33297 probes…

Microarray Normalization xps Microarray Normalization xps

updated 16.6 years ago • Michael Walter

<div class="preformatted">Hi, Working with the Illumina Human WG6 chips, and lumiHumanAll.db. After linear model fitting and clustering, I have identified a cluster of ~130 loci that show an interesting profile. However, as 125 of them have no GeneName or EntrezID, I am struggling...the Illumina Human WG6 chips, and lumiHumanAll.db. After linear model fitting and clustering, I have identi…

Clustering GOstats Clustering GOstats

updated 17.6 years ago • Al Ivens

retained introns and counted reads over them. I have named the retained introns so that they can be identified later. I know that when you build a DEXSeqDataSet, for each exon and library, the counts matrix contains the number...of reads in that exon and the number in all other exons. Thus, this suggests that I should be able to subset the DEXSeqDataSet to only contain the retained

dexseq

updated 10.5 years ago • i.sudbery

age, PMI, RIN, RIN^2, mapping rate, batches....). Obviously, I should only include a limited number of those variables. And how could I choose these variables? How the number of my samples would restrain my selections...PC1 is mainly dominated by a single factor(such as Batch), then (PC2,PC3, etc) may also be used to identify other factors.  Any suggestions? (I know this is not a pure …

deseq2 rnaseq

updated 7.1 years ago • Raymond

So I am trying to upgrade bioconductor and I get the error: \`Bioconductor version 3.4 is too old for R version 3.4.1; see https://bioconductor.org/install/\#troubleshoot-biocinstaller\` I follow the suggested...Run `` biocValid() `` to ensure your installed packages are valid for the current version of _Bioconductor_, and follow the instructions it gives you. The pr…

software error

updated 8.5 years ago • spevdo

<div class="preformatted"> I am looking to identify differentially expressed genes from five different cell types with five, five, four, four, and three affymetrix replicates...div class="preformatted"> I am looking to identify differentially expressed genes from five different cell types with five, five, four, four, and three affymetrix

Preprocessing gcrma Preprocessing gcrma

updated 21.6 years ago • Luckey, John

of 4 proteins one by one by linear regressions. However, because 4 proteins would be much smaller number than usual application of lmFit, I would like to ask for your input if there is reasons that lmFit may not be suitable

lmFit

updated 4.6 years ago • AyHi

Dear All, Recently, I found the mouse gene annotation in biomart had been changed to the version GRCm38 (mm10). However, I want to use mm9 version. Could anyone give some suggestions about how to do this? My code is mart...ensembl",dataset="mmusculus_gene_ensembl") Thanks! Best all! David! [[alternative HTML version deleted]] </div

Annotation biomaRt Annotation biomaRt

updated 13.3 years ago • lemon tree

div class="preformatted">Why is the affy version in the developmental packages 1.1 now? A couple of months ago it was 1.2 </div

affy affy

updated 23.1 years ago • Isaac Neuhaus

Hi,I am a PhD student and i would like to know if it is possible to find online the previuos versions of DESeq2 and where.Thank you. Best regards. Riccardo

DESeq2

updated 10.0 years ago • ribioinfo

gene counts table with ~50000 genes while now I have about half. Is it possible to see which version of the gene annotation I am using? Is it possible that the difference in the overall amount of genes could be that there...ago contains thousand of gene names that are similar to AC253536.2 (they all start with AC) but the version I am using now does not output any gene names like this. Does anyon…

tximport rna rnaseqGene biomaRt

updated 4.0 years ago • st3472

When trying to install riboSeqR with BiocManager (as shown below), I obtain the error "package ‘riboSeqR’ is not available for Bioconductor version '3.17'" (as shown below). ``` > BiocManager::install("riboSeqR") 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: ht…

Bioconductor riboSeqR

updated 2.7 years ago • Javier

I have been preprocessing in R a big data set in order to identify possible differentiated genes for two conditions. My main problem-question is, as i searched in literature, some...are totally(or in a significant persent) absent in their arrays. On the other hand, an important number of methodologies after normalization and quality control, use various implementations of non-specific filtering

bioconductor differential gene expression independent filtering

updated 11.0 years ago • svlachavas

div class="preformatted">Hello, Triggered by the paper by Andrew Jaffe et al. on bump hunting to identify DMRs, I tried to analyze one of our Illumina 450K datasets using the bump hunting methodology implemented in the...because the effect size in my study is too small? - What exactly is the value of the cutoff used to identify a dmr reflecting? The help pages state that it is a t-statistic cu…

Normalization minfi Normalization minfi

updated 13.1 years ago • Guido Hooiveld

to get common alterations between my samples. These are all arguments from the package doc(latest version): segments is a data frame extracted from the "output" element of the object returned by segment of the package DNAcopy...are considered as altered span alteredHigh is a positive number between 0 and 1 specifying the upper resh- ol…

DNAcopy cghMCR DNAcopy cghMCR

updated 14.1 years ago • nac

qvalue") Warning in install.packages : package ‘qvalue’ is not available (for R version 3.5.0) > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra...10.12.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Libr…

qvalue NBPSeq

updated 7.5 years ago • Gary

today and it was not supporting even the examples in the manual. When I checked, I was using an old version (v 1.16.1). It was strange because I just installed it with: <pre> source("https://bioconductor.org/biocLite.R") biocLite...the manual. Why the biocLite function is installing this old version? Updated to [Erik Wright](https://support.bioconductor.org/u/7838/) an…

DECIPHER

updated 9.6 years ago • Vinicius Henrique da Silva

to access a previous release of Ensembl (63) but listMarts(archive=T) reveals only ensembl_mart versions 43-47. Has the support for archival versions of Ensembl been discontinued? I'm using R v. 3.0.1 and biomaRt 2.16.0. Best...student, Nick Goldman group European Bioinformatics Institute (EMBL-EBI) [[alternative HTML version deleted]] </div

biomaRt biomaRt

updated 12.3 years ago • Greg Slodkowicz

Different number of DE genes using edgeR and DESEQ2 Good morning to everyone, I'm trying to compare the DE transcripts results obtained...and DESEQ2 respectively). I obtained different results I'm quite perplexed about, both in terms of number and identity of differentially expressed genes found. ................ I'm not sure the two pipelines are exactly comparable. Before...summary(re…

edger deseq2 rnaseq de

updated 5.7 years ago • Raito92

Hi I'm confused about how to identify differentially expressed genes (DEGs) in a single-channel expt. Is it possible to identify DEGs without making...topTable(fit, coef=2) All DEGs are stored in tt However, when I looked up the limma user guide (version 2016) in section 9.6, the example used contrast.matrix. Can someone help? Thanks Eric. &nbsp

limma toptable makecontrasts contrast matrix

updated 8.5 years ago • hoe

Airlines can know the situation with the trip whenever and from anyplace when they keep the contact number of the carrier convenient. Accessibility of Telefono American Airlines 24 horas makes the undertaking of knowing

AmericanAirlinesTelefono

updated 4.4 years ago • oscarjack463

div class="preformatted">I am trying to figure out how to get the information about the number of stat_pairs used in the MAS5 computations for each probe set. THis information does not appear to be in the exprsSet

Normalization probe Normalization probe

updated 19.1 years ago • Julie Dickerson

process data from Illumina HT-12 v3 Expression BeadChips. I am slightly concerned about the average number of bead replicates present on the Illumina HT-12 chip, as opposed to the Illumina WG-6 chip. Each bead is replicated on...the HumanWG-6 chip. Would you still suggest using VST with the Illumina HT-12 chip data, given the number of bead replicates? Thanks for your help. Christina Markunas …

lumi

updated 10.0 years ago • Christina Markunas

div class="preformatted">Hi, My server is running Debian and the most stable version of R for Debian is 2.1.5. I decided to use "apititude install r-base=3.1.0" to install a backport version of R but that command

MEDIPS ChAMP MEDIPS ChAMP

updated 11.4 years ago • Chong Kim San Allen

Hi, I need to run an old version of edgeR 2.2.6. I found it on Bioconductor: https://bioc.ism.ac.jp/packages/2.8/bioc/html/edgeR.html The problem is...that when I install it, the package corresponds actually to a newer version 3.8.6: <pre> tar xzvf edgeR_2.2.6.tar /usr/bin/R --vanilla --args TMM BH tagwise 5 R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet...limma</strong> &l…

edgeR

updated 8.9 years ago • elena.capel

however I am currently stuck with using R2.7. Unfortunately, it is my understanding that the newest version of Bioconductor requires R 3.0. Presumably I can install an older version of Bioconductor to get this to work. My question...is really this: How do I install an older version of Bioconductor? For example, in R 2.7, if I try to install Bioconductor I get the following message: > …

updated 12.1 years ago • Guest User

 Hello everyone, I am having problems running diffbind count function. I keep getting the following error (running in R on Mac): <pre> > H3K9me3 = dba.count(H3K9me3, minOverlap=2) Error: Error processing one or more read files. Check warnings(). In addition: Warning messages: 1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) : all sche…

diffbind

updated 10.3 years ago • tassa.saldi

Hi all, My understanding is that DESeq2 should by default normalize for differences in the number of reads. However, I am concerned that the magnitude of this difference is a bit extreme and I wonder if a different and...is needed to account for this. I accounted for this in the design, but I still have such a high number of genes that are significant (~900 with padj < 0.01 out of ~3000…

deseq2 normalization

updated 5.7 years ago • jillian.waters

I have individuals at a given time-point from three different stages: Stage 1, 2 and 3 and I wish to identify differentially methylated CpGs in these groups. Stage 1 vs Stage 2; Stage 1 vs Stage 3 and Stage 2 vs Stage 3 I have preprocessed...my data and adjusted for batch effects. Following that, I have done PCA and regression to identify potential covariates and found blood cell estimates accou…

limma illumina450k lmfit

updated 9.1 years ago • DSP

div class="preformatted">Hi, I have used DEXSeq (version 1.2.0) successfully to find differentially expressed exons in RNA-seq data. Yesterday I upgraded DEXSeq to version...factor") is not TRUE Thank you in advance. Regards, Nirmala [[alternative HTML version deleted]] </div

DEXSeq DEXSeq

updated 13.4 years ago • Akula, Nirmala NIH/NIMH [C]

Hello, I was surprised to observe two unexpected clear peaks at 0 and 5 in the raw copy numbers distribution, so I looked at the code and found this: <pre> setMethod("CA", signature=signature(object="CNSet"), function...Hello, I was surprised to observe two unexpected clear peaks at 0 and 5 in the raw copy numbers distribution, so I looked at the code and found this: <pre> setM…

crlmm copy number

updated 10.8 years ago • kforner

probeNames(Data) PM<-pm(Data) MM<-mm(Data) Cb<-cbind(GN,PM,MM) But the Cb output doesn't identify probe pare numbers 1007_s_at 649 371 1007_s_at 952 1043 1007_s_at 1640 2892 1007_s_at 3505 4894 1007_s_at 3703...2188 1007_s_at 2822 1812 Of cause I could script for those identifiers but is there a simple way to reproduce m…

probe probe

updated 19.7 years ago • DMITRY GRIGORYEV

Dear All, I would like to perform copy number variation analysis using conumee package in R, mainly to get the copy number plots. I had a few questions with respect...Dear All, I would like to perform copy number variation analysis using conumee package in R, mainly to get the copy number plots. I had a few questions with respect to that and I hope to get some help. 1. In the conumee v…

CopyNumberVariation CopyNumberPlots

updated 4.8 years ago • shweta

Hi everybody, my question is the following.. I have a sample of galaxy radial velocities in a galaxy cluster (unfortunately the size of this sample is N=18, I know..N<20 is not the best) and I wish to know what is the number of Gaussians which fit my data distribution in the best way [this can assume the values G=1:3]. Afterthat, I want to know what...Hi everybody, my question is the …

software error microarray probe annotation

updated 6.9 years ago • travascio.andrea91

<div class="preformatted">Hi, I am attempting to update DESeq with the latest version in found in Subversion. I have downloaded the latest version of DESeq to my hard drive using: svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DESeq What steps do I take to incorporate the features of the new version into my existing DESeq package? Thank you very much for any help. b…

DESeq DESeq

updated 13.8 years ago • Christopher T Gregg

expression-level uncertainty information into DEG detection. We recommend using the mmgMOS method to identify expression levels and standard errors of these levels, but there is no reason why you couldn't use the standard errors...version. Best regards Richard -- Richard Pearson School of Computer Science, University of Manchester, Oxford Road, Manchester...thread http://article.gmane.org/gman…

Microarray Clustering cdf probe affy affyPLM mmgmos Microarray Clustering cdf probe

updated 18.9 years ago • Richard Pearson

and 390 control samples and limma gives different results when I randomly select an equivalent number of control samples ? I read that imbalance sample size has a significant effect on identifying differential expressed

RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize

updated 23 months ago • Shaimaa Gamal

div class="preformatted">Good afternoon, I?m planning to conduct a study aimed at identifying and, if possible, quantifying members of the gut microbial community in broiler chickens, using the microarrays...Universidade do Estado de Santa Catarina UDESC - www.cav.udesc.br Lages - SC - Brazil Linux user number 487797 </div

Microarray SANTA Microarray SANTA

updated 16.3 years ago • Marcelo Laia

div class="preformatted">Hi All I am working on Illumina HumanOmni5MExome-4v1-1_A SNP array to identify CNV's and LOH's from this data. I have come across "crlmm" package that can do this and started following the "Preprocessing...and Genotyping Illumina Arrays for Copy Number Analysis" vignette. I realized that the crlmm package does not include CDF annotation for this Illumina array. I tried

SNP Annotation cdf SNP Annotation cdf

updated 11.8 years ago • Venu Pullabhatla

Error in align(index = "ht", readfile1 = reads1, readfile2 = reads2, input_format = "FASTQ", : The number of input file names is different from the number of output file names

align Alignment subread

updated 3.7 years ago • saira

rerunning code that my colleague originally wrote and ran in 2012.  Originally, 379 sites were identified as significantly different between groups (0.05 level of significance).  However, when I run the code now, I...identify 5,711 sites.  The sites originally identified are included, and overall they are the more significant sites...most are included in the to…

sva combat

updated 10.3 years ago • anne.bozack

all, I was wondering if there are any plans to update the `` mirbase.db `` package. The current version (1.2.0) bases on miRBase version 19. Thanks, jo

mirbase.db

updated 10.1 years ago • Johannes Rainer

Hello ... Going back to an earlier discussion, if people do find the need to use older versions of the metadata packages (e.g. 1.4.0 of GO), please let me know and I will send them to you. Thanks -J</div

updated 21.8 years ago • Jeff Gentry

Hi Michael, I used DESeq2 version 1.4 on some RNSeq data four month ago, and repeat the analysis within version 1.5 last week on the same dataset. I got...pretty much the same DE gene lists (>90% overlaps), only the fold changes looked much shrunk from version 1.5. We have some rtPCR data correlated better to the old fold change ranges though. I am aware of you’d changed the beta

deseq

updated 11.3 years ago • Yuan Hao

ask for advice, please let me know if I should look somewhere else. I am currently working on a new version of a Bioconductor package and I think I am now ready to submit it. I am not the maintainer of the old version package (but...add me as an author of the package? if so, how? 2) Can somebody explain to me how to submit the new version? I already looked in the Bioconductor website and I fou…

package submit package package updates

updated 9.5 years ago • francescodc87

through SomaticSignatures package. I am trying to use assesNumberSignatures function to determine number of signatures. I entered the following commands: > n\_sigs = 2:8 > gof\_pca = assessNumberSignatures(cancer\_mm, n\_sigs

assesNumberSignatures SomaticSignatures package

updated 9.4 years ago • arsala521

to determine rank. It seems like the more ranks I use the "better" fit. i suppose with the small number of samples i have there really can't be more than 2 or 3 signatures. Also as i look at the samples contributing to the signatures

somaticsignatures

updated 10.5 years ago • chang02_23

we downloaded and installed the annotation package for hgu133a to ensure that we have the latest version. Thank you for providing the PubMed identifiers. We notice a redundancy for the following example: > library(annotate...1] "95045392" "20530220" "11078474" "7957066" When we go to PubMed, and type in the above identifiers, we find that 95045392 is the same document as 7957066, and …

Annotation GO hgu133a Annotation GO hgu133a

updated 21.3 years ago • Lynn Young

out the ratio that I was interested in. However, I noticed that the samples I put in changes the number of significant genes a lot even when I only pull out the ko vs wt high vs mRNA ratio: <table border="1" cellpadding="1" cellspacing...fit2 <- eBayes(fit2) interaction_high_mrna <- topTable(fit2, coef = 'interaction_high_mrna', number = nrow(count_mat_filtered)) sum(inter…

limma voom

updated 8.2 years ago • Jake

preformatted">Hello, I'm not sure how to retrieve GO terms associated with the NCBI accession numbers (such as "NM_172496"). I have found references to GOLOCUSID, but I cannot find this environment. I have GOstats and I can...access GOTERM, but not GOLOCUSID. Anyways, I also failed to map NCBI accession numbers to Entrez IDs using BioIDMapper: library(BioIDMapper) data(glist) > head…

GO GOstats GO GOstats

updated 15.6 years ago • January Weiner

When you say "getting it wrong" do you mean that people who have computed their data using an older version of "affy" (or are still using an older version) were getting it wrong? BTW, what do you mean with "The "RMA" brand name has been...of RMA in XPS has implemented the correct RMA algorithm, as verified earlier with older versions of affy. The same holds true for APT. Best regards Christian …

Normalization affy preprocessCore xps Normalization affy preprocessCore xps

updated 16.5 years ago • cstrato

Hi, I used celegans.db_2.3.5 to convert affy ID to WormBaseID. Could you please let me know the version of wormbase (e.g. WS180, WS200, etc..) that was used for celegans.db_2.3.5? Thank you very much for your help! Kind regards

celegans affy convert celegans affy convert

updated 15.3 years ago • Julie Zhu

value < 0.05 as opposed to the 30 genes I was getting before with the same comparison. The sample numbers or anything else for my __D1__ and __D2__ groups haven't changed at all, I've only added the __H__ samples. Please see...eBayes(fit2)</pre>   I was wondering if anybody knew the reason for this discrepancy in the numbers of significant genes (with adj.P-value …

limma differential gene expression microarray linear model

updated 10.5 years ago • bcbio_uk

Hi, I have been trying to install cummerbund on R version 3.0.2 (2013-09-25), but I receive the following error: <pre> * installing *source* package ‘RCurl’ ... ** Paket ‘RCurl’ erfolgreich...Hi, I have been trying to install cummerbund on R version 3.0.2 (2013-09-25), but I receive the following error: <pre> * installing *source* package ‘RCurl’ ... ** Paket ‘RCurl’ erfolgrei…

cummerbund

updated 9.5 years ago • gupta

I get the following error message: package ‘GenomicAlignments’ is not available (for R version 3.1.2) Is there a work around or when will the package be updated for the latest version of R? Thanks, -David

genomicalignments

updated 10.9 years ago • david.dekoeyer

Hi,   Gviz is an amazing package. But I found that the junction numbers reported from sashimi plot were quite different from the junction numbers generated by “summarizeJunctions” command...from GenomicAlignments package. I got junction numbers with following codes:   \# Gviz library(Gviz) afrom<-2960000 ato<-3160000 alTrack <- AlignmentsTrack(system…

gviz genomicalignments

updated 10.0 years ago • chengwang29

mine have previously worked with Genome Studio, and they performed quality control by comparing the number of detected CpG islands satisfying detection p-value of 0.05 and 0.01 between all the samples. To be clear, after preparing...CpG islands with p-value < 0.01 for each analysed sample, whilst another column reported the number of detected CpG islands with p-value < 0.05 for e…

RnBeads

updated 4.8 years ago • Federica

I don't have sudo, my R version is 4.0.2, I can not use BiocManager::install, because it notices me the version is not compatible. However, I can not degrade...the Bioconductor version. Here is the problem capture: ``` >BiocManager::install() Error: Bioconductor version '3.14' requires R version '4.1'; use `BiocManager...install(version = '3.12')` with R version 4.0; see https:/…

BioManager

updated 3.7 years ago • liqidong52

I am trying to annotate the data (with gene name and gene symbol) from __\[HuGene-1\_0-st\] Affymetrix Human Gene 1.0 ST Array \[transcript (gene) version\]__ platform using __hugene10sttranscriptcluster.db. __ I use the following script to get the gene symbol. <pre...and gene symbol) from __\[HuGene-1\_0-st\] Affymetrix Human Gene 1.0 ST Array \[transcript (gene) version\]__ platfor…

bioconductor hugene10sttranscriptcluster.db annotation

updated 8.8 years ago • Khawaja

here. I have 4 different point mutations that are __mutually exclusive__ and I wish to identify DE isoforms specific for each mutation. Additionally, I have reason to believe that the mutations cause similar...differential expression for some isoforms and I also wish to identify those. __My questions are:__ * What is the best approach to identify the differences and the sim…

limma limma-voom limma design matrix confounders

updated 7.5 years ago • S.Bamopoulos