Bioconductor Forum

CHARM) on 450k data but when I try to apply dmrFdr to the output from dmrFinder, it does not seem to identify the array annotation package. I have tried package="IlluminaHumanMethylation450k.db" and also package="IlluminaHumanMethylation450kmanifest...right annotation package for 450k data in dmrFinder. Thanks, Khadeeja [[alternative HTML version deleted]] </div

Annotation Annotation

updated 13.2 years ago • khadeeja ismail

Total number of duplicates in ChIPQC differs from multiqc ? I check all chromosomes not just one... In fact 0 duplicates are found with

ChIPQC ChIPQCreport

updated 8.6 years ago • ZheFrench

packages/3.15/bioc/src/contrib/Archive/S4Vectors/ How can I download `S4Vectors` version `0.34.0

S4Vectors

updated 20 months ago • bounlu

diagnostic test for outliers called Cook’s distance caused DESeq2 (version 1.10 vs 1.30) have big different result? anyone find similar issue

version1.30 version1.10 deseq2 DESeq2

updated 4.3 years ago • Shicheng

div class="preformatted">Hi, Custom cdf R package version 12.0.0 is upgraded to 12.1.0. It is compatible with R 2.10.z and Bioc 2.5 now. Best, Manhong </div

cdf cdf

updated 16.1 years ago • Manhong Dai

have added minoverlap with default 1 bp to both findOverlappingPeaks and makeVennDiagram for the dev version with revision 65860. For a diagram generated from two datasets A and B, there are 4 numbers, i.e., nA: number of peaks unique...to A, nB: number of peaks unique to B, nAB: number of peaks shared in A and B, totalTest nA nB nAB. Best regards, Julie On 5/11/12 8:06 PM, "Sukhdeep...…

ChIPpeakAnno ChIPpeakAnno

updated 13.6 years ago • Julie Zhu

Running into an error of not being able to install or run fgsea in R Version 1.4.1106. ``` # library(fgsea) Error: package or namespace load failed for ‘fgsea’ in loadNamespace(i, c(lib.loc, .libPaths...Running into an error of not being able to install or run fgsea in R Version 1.4.1106. ``` # library(fgsea) Error: package or namespace load failed for ‘fgsea’ in loadNamespace(i, c(lib.…

r fgsea

updated 3.9 years ago • amir.khan

anyone have an idea how to do that? Thanks in advance Dolev Rahat sessionInfo(if required): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE...1.1 stats4_2.15.1 stringr_0.6.1 tools_2.15.1 zlibbioc_1.2.0 [[alternative HTML version deleted]] </div

updated 13.3 years ago • d r

Upon installing the latest version of ChIPQC (1.12.1) in a new R 3.4.0 installation, I encountered a few different errors upon running `` ChIPQCreport ``. These...various errors were all resolved, once I upgraded DiffBind to the latest version (2.4.4). ChIPQC should therefore install the latest available version or try to upgrade any present versions upon

chipqc diffbind chipqcreport

updated 8.5 years ago • Coby Viner

splicing functions within limma as outlined in the user guide. I've updated to the newest version of limma today and it looks like the functions topSplice() and plotSplice() have now been removed from the package (within...plotSplice() Error in plotSplice() : could not find function "plotSplice" > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Runn…

limma

updated 8.2 years ago • gmuir

Does any one know a R package designed for genetic analysis of VNTR (variable number of tandem repeats) genotype data? For example, performing Hardy Weinberg equilibrium test, calculating heterozygosity

R package

updated 6.0 years ago • ycding

PANTHER.db package](https://bioconductor.org/packages/release/data/annotation/html/PANTHER.db.htm) version 1.0.4 (as by February 2019) contains PANTHER database version 12.0 (released on 2017-Sep15). However, according to [PANTHERdb...website](http://www.pantherdb.org/data/), the latest PANTHERdb is Version 14.0, released on 2018-12-03, generated from the 2018_04 release of [ReferenceProteome …

PANTHER.db update annotation go

updated 6.9 years ago • alfonsosaera

There is currently a mismatch between the source (2.55) and binary (2.56) versions of the rGADEM package on the bioc release page. Is this expected? Who can I notify to fix if not? https://bioconductor.org

rGADEM

updated 6 months ago • Jay hesselberth

<div class="preformatted">Hello, I have some problems with the gcrma normalization procedure. Please look at the output: ---- > Chips.norm<-gcrma(Chips.raw) Adjusting for optical effect............................Done. Computing affinities.Error in get(x, envir, mode, inherits) : variable "mouse4302dim" was not found > traceback() 9: get(nam) 8: get("NROW", get(nam…

Normalization cdf gcrma Normalization cdf gcrma

updated 18.4 years ago • Sebastian Bauer

I have a smallRNA sequencing data from two samples, without replicates. I tried using DESeq to identify differentially expressed gene following the manual, and the code is as below: > library(DESeq) > conds <- c("NSC", "TSC...256 265 1.0351562 0.049848549 0.012192131 0.9696484 NA NA > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 local…

Sequencing miRNA SmallRNA DESeq Sequencing miRNA SmallRNA DESeq

updated 15.0 years ago • Wu, Xiwei

div class="preformatted">Hi Ingrid, You can use lumiHumanAll.db package, which includes all versions and releases (from version 1 to 3) of Illumina Expression chips. As the Illumina identifiers may have slight differences...even across different releases of the same version, I recommend use this library. You do not need to worry which version or release it is because the package are nuID inde…

Annotation lumi Annotation lumi

updated 17.7 years ago • Pan Du

class="preformatted">Philippe -- Biobase is using 'numeric_version', which is available only in a version of R later than the one you are using. Update R. Martin phguardiol at aol.com writes: > Dear BioC users, > > I have recently...downloaded the dev version of affy and gcrma libraries (cf infra), as well as the dev metadata I need (cf infra) and when I launch a justGC…

hgu133plus2 cdf Biobase affy affyio hgu133plus2 cdf Biobase affy affyio

updated 18.3 years ago • Martin Morgan

However, I am trying to install the bioconductor package BayesPeak and it requires bioconductor version 2.6 or later How do I upgrade the Bioconductore package? I have run: |source("http://bioconductor.org/biocLite.R") update.packages

BayesPeak BayesPeak

updated 14.3 years ago • Mary Ellen Fitzpatrick

Before installing DASC, you need to install three dependent packages: NMF, CVxClustr, and Biobase. What version of R is required? This is the error I received when installing the NMF dependent package. Error in loadNamespace(j &lt...installing DASC, you need to install three dependent packages: NMF, CVxClustr, and Biobase. What version of R is required? This is the error I received w…

DASC

updated 5.3 years ago • 1494309230

div class="preformatted">Dear all, I tried to update the package ggbio from version 1.0.4 to the current release version 1.2.8 but there seems to be an error. I list below the error output and sessionInfo...I tried also to use the development version (1.3.4) but I get the same problem. Best regards > source("http://bioconductor.org/biocLite.R") BiocInstaller version...1.4.3, ?biocLi…

BiocInstaller ggbio BiocInstaller ggbio

updated 13.7 years ago • Juan L. Mateo

div class="preformatted">Hi, is there any way to retrieve the information about the version/date of the source that was used for the annotation package in addition to the date for the generation of the package

Annotation Annotation

updated 18.9 years ago • Ido M. Tamir

are usually appropriate for larger libraries. As a general rule, a good threshold can be chosen by identifying the CPM that corresponds to a count of 10, which in this case is about 0.5_: "__  <pre> cpm(10, mean(y$samples$lib.size...samples$lib.size)) expressed <- rowSums (cpm(y) > cpm.filter) >=N/2 # where N the total number of samples y2 <- y[e…

edger cpm non-specific filtering rnaseq

updated 7.5 years ago • svlachavas

If I want to retrieve the identifier of a protein in Reactome using the ENTREZ id I can't, both the PATHID and the REACTOMEID are the same. While if I understood...correctly they should be different, REACTOMEID, would be the identifier for such protein and PATHID the identifier of the pathway where such protein is involved. <pre> >library("reactome.db...1 3855 R-HSA-1266738 2 …

reactome.db

updated 8.4 years ago • Lluís Revilla Sancho

Regards, Avril Avril Coghlan University College Cork, Ireland [[alternative HTML version deleted]] </div

Network Network

updated 15.9 years ago • Coghlan, Avril

Cashe C U S T O M E R Care Number ♻️ 86√88√20√26√65 💍 09832330695 Call Now All REfound 08688202665 Call Cashe C U S T O M E R Care Number ♻️ 86√88√20√26√65 💍 09832330695...Call Now All REfound 08688202665 Call Cashe C U S T O M E R Care Number ♻️ 86√88√20√26√65 💍 09832330695 Call Now All REfound 08688202665 Call Cashe C U S T O M E R Care Number ♻️ 86√88√20√26√65 💍 09832330695

GRaNIE hu6800probe InteractiveComplexHeatmap lpNet MetID

updated 2.6 years ago • hdss

gt; >>> Hi, >>> >>> I have a special request regarding PGSEA Package to identify >>> downregulated >>> genes. I am not clear about this line >>> subtype<- gsub("\\.", "_",gsub("subtype: ", "", >>> phenoData...Medicine >>> &a…

GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase

updated 13.9 years ago • Valerie Obenchain

wrote: > Hi, > I'm not using your library but I think your problem is different to a version > problem. If your libSBML is correctly installed, I advise you to search on > your system where really is the shared...of rsbml then worked fine, but ldd shows that the rsbml.so file then actually links to the local version: merlin ~> ldd /usr/lib64/R/library/rsbml/li…

rsbml rsbml

updated 15.9 years ago • Rainer Machne

iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi,=20 Can anyone help create the Mac versions of the data packages? Thanks. Charles Chunfa (Charles) Jie Charles Jie, Ph.D./ M.S.=20 JHMI Microarray Core School of Medicine...size="3D2"></font> </div> <div><font face="3DArial" size="3D2">Can anyone help create the Mac versions = of the data=20 package…

Microarray Microarray

updated 23.2 years ago • Chunfa Charles Jie

We are using imagene files and we can generate maQualityPlots and set a badspotfunction parameter to identify bad spots. This allows us to see on a spatial plot flaged spots as black sqaures. Do you have any suggestions as what...How does arrayQualityMetrics handle missing values? regards Louise [[alternative HTML version deleted]] </div

arrayQualityMetrics arrayQualityMetrics

updated 16.8 years ago • Louise Donnison

have a list of ChIP seq- CTCF binding peaks for mouse. I was wondering what would be the best way to identify if any peaks lie within 1000 bps upstream or downstream of known exons (obtained from the ref seq table, ucsc genome...import the exon positions directly into R? Thanks in advance, Kavitha [[alternative HTML version deleted]] </div

updated 13.9 years ago • Kavitha Mukund

genome. I am wondering if there are bioconductor packages, and/or other software that can help me identify the insertion sites. I would also like to pick your brains on how to go about doing this, what is the optimal protocol...that is. Thanks a lot for your help, Al [[alternative HTML version deleted]] </div

GO

updated 11.3 years ago • Alpesh Querer

<div class="preformatted">Dear Sir or Madam, I have a question about performing PCA method on the gene expression data. If I have a training dataset and I identified a smaller set of genes as biomarkers to predict case and control status.... What if I only select those genes from the...question about performing PCA method on the gene expression data. If I have a training dataset and I iden…

updated 14.8 years ago • Xiaowei Guan

I tried to map genes to biocarta pathways using cMAP package, but I found that the molecule identifiers provided by cMAP functions are quite different from that given in the biocarta pathway website or cMAP pathway...m wondering when it will be fixed. Thank you for your attention. Ahrim [[alternative HTML version deleted]] </div

Pathways Pathways

updated 16.7 years ago • Youn, Ahrim NIH/NCI [F]

div class="preformatted">Hi all, I d like to know if there is a package in BioC that can identify genes that are differentially expressed between 2 conditions and analyze their distribution along the chromosomes...loss or gain of chromosomes from the microarray data... thanks Philippe [[alternate HTML version deleted]]</div

updated 22.7 years ago • Phguardiol@aol.com

quantiles [shinySummarize] Computing principal components summary Object: shinyMethylSet Number of samples: 137 Phenotype: 22 covariates Origin object: RGChannelSet Array: IlluminaHumanMethylation450k runShinyMethyl...summary) Error in object@greenControls[[i]][, o] : incorrect number of dimensions

shinyMethyl minfi

updated 4.7 years ago • jefflincoln4

<div class="preformatted"> Hi to all, I'm dealing with a problem that looked so simple, but I'm able to solve... I have a list of gb accession numbers: for example: "M57423" "Z70218" "L17328" "S81916" "U63332" "M77235" and I would like to find ( in a repository for ex.) the names as: [1...with a problem that looked so simple, but I'm able to solve... I have a list of gb accession num…

annotate annotate

updated 19.7 years ago • Giulio Di Giovanni

due to technical reasons, I had to remove some of the control condition (only 3) due to a low number of reads (<5e6). This means that I have some "unpaired" samples, i.e. they received the treatment but I have no control for...it correct, that after using this approach, I can remove the `patient.id` from my design because the identified surrogate variables account for patient-specific effe…

edgeR DifferentialExpression

updated 20 months ago • nhaus

available (GSEA or GSA) accomadate such one-class data without modification? We also wish to identify individual genes whose mean d-statistic is not zero. I have suggested using a t-test with n=number of experiments with

PROcess PROcess

updated 18.8 years ago • Mark W Kimpel

<div class="preformatted">Dear all, I made a pipeline to analyse Illumina beadarray. I tried to install my pipeline in a new computer. I use a filter based on the illuminaHumanv4PROBEQUALITY function of the illuminaHumanv4.db package. In the new computer this step don't work because some id are missing. I found that the problem comes from illuminaHumanv4ARRAYADDRESS function that I need to…

beadarray beadarray

updated 13.4 years ago • Amos Kirilovsky

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

lpNet

updated 2.6 years ago • Udihvd

KEGGSOAP package, especially why the "bconv" utility is not integrated, which allows to map foreign identifiers on KEGG identifiers. With "bconv" it would be easy for me to map hgu95av2 probe IDs on ENSEMBL/UNIGENE/UNIPROT/etc...In addition, the original mark.pathway.by.objects function from the KEGG API allows to put in EC numbers which is not supported by the corresponding KEGGSOAP function. Co…

Pathways hgu95av2 probe KEGGSOAP Pathways hgu95av2 probe KEGGSOAP

updated 15.9 years ago • Ludwig Geistlinger

tool is only based on genome annotation and how to remove "potential dead cells - signified by high number of mitochondria). But have seen several papers where scater has been used to do something like the one I would want to

SingleCellExperiment

updated 3.5 years ago • otieno43

Thanks in advance!__ Warning message: package ‘DESeqDataSetFromMatrix’ is not available (for R version 3.4.1) __Here's my session info__ R version 3.4.1 (2017-06-30) Platform: x86\_64-w64-mingw32/x64 (64-bit) Running under: Windows...BiocInstaller\_1.26.0       loaded via a namespace (and not attached): Error in x\[\["Version"\]\] : subscript out of bounds…

deseq2

updated 8.3 years ago • alkimistdoc

Hi Steffen and other biomaRt gurus I can't see an option in useMart(), but can I specify the version (eg ENSEMBL 39 not 40) Thanks Aedin -- Aed?n Culhane Harvard School of Public Health, Dana-Farber Cancer Institute </div

Cancer biomaRt Cancer biomaRt

updated 19.3 years ago • Aedin Culhane

Developers and Users, I'm using some of the Bioconductor packages to analize Illumina 450k data for identifying differentially methylated positions/sites and Genes associated with these ones. With the IMA package version...get from lists indexed by the Cg ID (I got some lists of this type by dmpFinder in the Minfi package version 1.8.9) as many lists indexed by Genes Symbols/Names associated wi…

minfi minfi

updated 11.7 years ago • Giovanni Calice

Hi, I have the following command which always worked well, until now.      txdb <- makeTxDbFromGFF("/path/to/gencode.v19.annotation.gtf", dataSource="Gencode", organism="Homo sapiens", format="gtf") Now I get the following output:      Import genomic features from the file as a GRanges object ... OK  &a…

software error R bioconductor genomicfeatures error message

updated 8.8 years ago • Walter F. Baumann

downloaded\_packages Warning message: package ‘DESeqDataFromMatrix’ is not available (for R version 3.4.0)"   I tried downloading and running three different versions of R, 3.3.2 / 3.4.0/3.5.1, but no luck. I have also

DESeq2 deseqdatasetfrommatrix r new version

updated 7.3 years ago • megannj

1 Gene 2 . . The question of interest is to compare results before and after treatment and thus identify genes of interest, classify patients, and identify patients who respond to the surgery. Also, the sample size needed...new to microarray analysis. Any reply is sincerely appreciated. Haiyan [[alternative HTML version deleted]]</div

Microarray Bayesian Microarray Bayesian

updated 21.7 years ago • Haiyan Wu

Hello, I've noticed that the number of variables included in the data matrix influence the Wald statistic and fold change values in the DESeq2 output...Hello, I've noticed that the number of variables included in the data matrix influence the Wald statistic and fold change values in the DESeq2 output. I don't understand why is this so. The data set I'm using is from a very simple design: 1 tre…

deseq2

updated 9.5 years ago • szoboszlay.m

please also include the results of running the following in an R session Credit Bus Customer care number 9040723742//8777638488 Call Now sessionInfo

CreditBusCustomercarenumber9040723742//8777638488CallNow

updated 2.6 years ago • Rahul Sharma

of running the following in an R session sessionInfo( ) ``` QUICK MONEY LOAN CUSTOMER CARE NUMBER📞 7250536107 ☎️ 7250536107 CALL

Mumbai

updated 2.6 years ago • Salks

of running the following in an R session sessionInfo( ) ``` QUICK MONEY LOAN CUSTOMER CARE NUMBER📞 7250536107 ☎️ 7250536107 CALL

GRaNIE MetID

updated 2.6 years ago • Salks

installation of a package (GO.db) fails due to a dependency (AnnotationDbi) not having the correct version, even though in fact it is the latest available version. The dependency loads fine and shows properly in sessionInfo...other packages. Thanks for any advice on how I may solve this problem. Alex ```r R version 4.3.1 (2023-06-16) -- "Beagle Scouts" > .libPaths("/proje…

AnnotationDbi GO.db

updated 23 months ago • alexandre.blais

Dear Bioc Community, for some functionality issues, i would like  to install an older specific version from an R package that is "hosted" on the Bioconductor repository. If i remove the current version, is this possible via...biocLite() and using the specific version i would like to install, or a different approach is recommended ?? Best, Efstathios

Bioconductor biocLite R packages oldversion

updated 10.1 years ago • svlachavas

on Mac using R Studio, but it shows the warning: package ‘chorddiag’ is not available (for R version 3.6.1) Could you please help to solve this problem? Many Thanks Jack Nguyen

software error

updated 6.3 years ago • Jack

21000000,name = "ENSEMBL") Fehler in .getBiomart(genome) : Gviz thinks that the UCSC genome identifier 'gasacu1' should map to the current Biomart head as 'BROADS1', but its current version is 'BROAD S1'. Please manually...or than later in my workaround.  Best wishes and thanks a lot.  sessionInfo() `` R version 3.3.2 (2016-10-31) `` `` Platform: x86_64-apple-darwin13…

Gviz-package biomart plottracks ucsctrack stickleback

updated 8.8 years ago • br

I guess dispersion changes so results change slithly ? thanks, anna -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252

updated 13.2 years ago • Guest User

pairs. The yeast2.db and yeast2probe package's don't seem to help me. Where can I get probe level identifiers for this platform. Any help very appreciated! Omri Yahel MSc Student School of Biological Sciences University...of Auckland, New Zealand [[alternative HTML version deleted]] </div

yeast2 probe yeast2 probe

updated 17.0 years ago • Omri Yahel

Yeast 2.0 chip. There are 30 time-points with no replication. Is there any package I could you to: - identify genes with significant expression changes through the 30 points - cluster the significant genes and visualize...Thank you very much for any suggestion/help! Cheers, P. [[alternative HTML version deleted]] </div

Microarray Microarray

updated 16.9 years ago • Paco Recca

div class="preformatted">Hello all, I install R 2.7.0 + BioC 2.2 devel version on a Mac OS 10.4 server. I have problem in loading Rgraphviz package. Note that I have already downloaded and installed...graphviz-2.12.dmg, and Rgraphviz was installed from source. Is it because I need a newer version of graphviz? I tried installed Graphviz 2.14. And I still got the same error message. Any ideas? T…

graph Rgraphviz graph Rgraphviz

updated 17.7 years ago • Luo Weijun