Bioconductor Forum

Dear Bioconductor community, based on a recent analysis of an RNA-Seq gene expression analysis concerning different cancer cell lines, i was trying to apply the relative Treat methodology for various biological contrasts of interest, in order to narrow my DEGlists, as significant differences have already be identified in the relative MDS plots and EDA analysis. Based on the downstream code c…

edger differential gene expression glmtreat

updated 7.2 years ago • svlachavas

preformatted">Hi, I am a beginner user of R and trying to install "IRanges" package. I have R version 2.11 and running it on Mac OS X 10.4.11. It always gives out this error: gcc -std=gnu99 -I/Library/Frameworks/R.framework...on how to solve this will be very much appreciated. Thanks! -Lilyana [[alternative HTML version deleted]] </div

updated 15.6 years ago • Lilyana Margaretha

div class="preformatted">Illumina microarray users, We just found Illumina released Human version 3 Expression BeadChip and the numeric ProbeIDs are totally different from previous versions. If you are using Illumina...annotation packages, please make sure the version is correct. We will try to create new version of annotation packages compatible with old versions as soon as possible

Microarray Annotation Microarray Annotation

updated 17.7 years ago • Pan Du

features and 50 samples. I am looking for clusters of samples. There is a clear division in a small number of features (3-4) indicating the existence of subgroups, and a much less clear situation in many other features. Pvclust...two clusters can be seen, but are not clearly divided. If I assign the samples to the clusters identified by pvclust and apply randomForests, I can distinguish between …

ASSIGN ASSIGN

updated 15.1 years ago • January Weiner

Hi there, I'm trying to import a "loom" file with the devel version and I'm getting an error: ``` >library(LoomExperiment) > scle <- LoomExperiment::import("l5_all.agg.loom", type="SingleCellLoomExperiment...TRUE, : invalid [[ subscript type: NULL ``` This same command works perfectly with R version 3.6. Does anyone have any clue? Thanks ``` >…

LoomExperiment

updated 5.7 years ago • marc.tormo

div class="preformatted">Hello, I am using RankProd to identify differentially expressed genes between mouse and human arrays, where the human genes are represented as the homologous...reading the original paper we weren't so sure. Thank you, Adam Cornwell [[alternative HTML version deleted]] </div

RankProd RankProd

updated 13.0 years ago • Cornwell, Adam

all, I have a microarray dataset compiled from several sources, so I am facing some challenges with identifying the expressed genes of each cell type. I am thinking to use the enriched gene sets of each cell type as the expressed...tool for the analysis of one cell type only. Thank you, Wendy [[alternative HTML version deleted]] </div

Microarray Microarray

updated 14.2 years ago • Wendy Qiao

there a Bioconductor package that calculates this? Secondly, is there a bioconductor function that identifies outlier spot intensities among replicate arrays? Appreciate your response. Anjan -- =================================== anjan purkayastha, phd. research...ma 02138 phone-703.740.6939 =================================== [[alternative HTML version deleted]] </div

Normalization Normalization

updated 15.3 years ago • ANJAN PURKAYASTHA

conflicts and I can't be able to run those packages since them. I'm trying to install different R versions as slot on Gentoo but without success until now. Also, I have trying to use the Illumina manifest files to map probe...to gene information, however, most of genes list were not identified. Any overcome to that is welcome.  Best       &nbsp

lumi lumiHumanIDMapping lumiHumanAll

updated 10.9 years ago • Frederico Moraes Ferreira

Hi, I'm working with a fungus that don't have its genome sequenced. I have a list of accession numbers from a blast of peptides obtained from a proteomics experiment, and each number come from a different organism. For...as in: org.Mm.egGO[mappedLkeys(egids)] is there a way to do this for a diverse group of accession numbers from different organisms? Assuming that I have my list of annotated…

GO Organism GO Organism

updated 12.1 years ago • Ricardo Silva

<div class="preformatted">In package affy version 1.2.27, there is a mistype error in the code of xy2indices : function (x, y, nr = NULL, cel = NULL, abatch = NULL) { if (any(x <= 0) || any(y &lt...div class="preformatted">In package affy version 1.2.27, there is a mistype error in the code of xy2indices : function (x, y, nr = NULL, cel = NULL, abatch = NULL) { if (a…

affy affy

updated 22.6 years ago • Pierre-yves Boëlle

div class="preformatted">Hello all! I was trying to convert RefSeq accession numbers to GenBank accesion numbers (or the opposite). I think that there must exist a library that does this job automatically...Does anyone know anything relevant to this? Thank you all, Eleni [[alternative HTML version deleted]] </div

convert convert

updated 17.6 years ago • Eleni Christodoulou

preformatted">Dear all, I managed reading in a kegg graph A graphNEL graph with directed edges Number of Nodes = 70 Number of Edges = 109 but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can I see the graph? Many

graph graph

updated 15.1 years ago • Yan Jiao

sets: invalid BroadCollection category: 'c8' ``` When I try to import XML files from an older version (e.g. v5.2 -- which doesn't have the `c8` category) I get no errors. Is there a way to get around this? ```r sessionInfo() R version 4.0.2...Catalina 10.15.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Vers…

GSEABase

updated 5.1 years ago • Ezgi

when using the simpleaffy package on Linux I don't have the qc function available (while the Windows version works well). Any suggestions how to solve this ? Thank you very much, Wolfgang Raffelsberger > sessionInfo() Version...2006 month 06 day 01 svn rev 38247 language R version.string Version 2.3.1 (2006-06-01) > > help(qc) No documen…

cdf genefilter affy affydata simpleaffy affyQCReport affyio cdf genefilter affy affydata

updated 19.5 years ago • Wolfgang Raffelsberger

div class="preformatted">Is there software for analysing copy number/LOH/deletions in SNP data using R/Bioconductor? Plus apologies for being slightly off-topic but Does anyone know what

SNP SNP

updated 19.4 years ago • Stephen Henderson

Would you think it is appropriate to use DESeq2 to normalise the counts for library size when the number of genes is so small? I am comparing mutant with wild type, the two genotypes have massive differences in plastid gene

DESeq2

updated 22 months ago • Suvi

I'm working with DESeq2 to make a DE analysis between samples in two different conditions. During the analysis, I identified a batch effect due to the sequencing time modelled as a covariate in the design formula. From the differential expression (Wald test), I was able to retrieve a good number of significant genes (~100) but the LogFC range looks not reliable going from -30 to +30. - What …

DESeq2

updated 3.9 years ago • save

Hi, Is there a way I can check the archive versions of bioamRt and then use one them to run. I have an old scripts from 2016, 2017 and 2018 and I want to rerun them with their...corresponding version of biomaRt. Thanks a lot. D

biomaRt Bioconductor

updated 6.5 years ago • Didi

<div class="preformatted">I have installed R version 2.3.1, on Mac (OS 10.4.7, on an Intel CoreDuo iMac). When I try to install bioconductor -- following instructions, using biocLite...div class="preformatted">I have installed R version 2.3.1, on Mac (OS 10.4.7, on an Intel CoreDuo iMac). When I try to install bioconductor -- following instructions, using...The downloaded packages are …

affy affy

updated 19.3 years ago • Debashis Bhattacharya

Dear Bioconductor Support, i recently tried to upgrade my R version to the newest R version 3.2 in one of my computers in order to check how it works: <span style="line-height:1.6">My current...info is : __sessionInfo()__</span> __R version 3.1.1 (2014-07-10) Platform: x86\_64-w64-mingw32/x64 (64-bit)__ __locale: \[1\] LC\_COLLATE=Greek\_Greece.1253  LC\_CTYPE...and…

bioconductor upgrade installr Windows8 R 3.2

updated 10.7 years ago • svlachavas

object ... OK Error in list(PKGTITLE = paste("Annotation package for", dbType, "object(s)"), : 'version' is missing In addition: There were 50 or more warnings (use warnings() to see the first 50) If I run this on RHEL5, the same...were 50 or more warnings (use warnings() to see the first 50) For OS X: > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin12.4.0…

TranscriptDb IRanges TranscriptDb IRanges

updated 12.3 years ago • Michael Steeves

Sierra 10.12.6. Thank you for any help. BiocManager::install("maEndToEnd") Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12) Installing package(s) 'maEndToEnd' installing the source package ‘maEndToEnd...file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/systemfonts/libs/system…

maEndtoEnd

updated 5.8 years ago • vlaufer

I am running a couple of different versions of R on Linux and Mac but have recently found that msaR has stopped displaying on recent versions of Chrome (Version...re-installed msaR and it is still not displaying on Chrome and Firefox. I happen to have an older version of Firefox (88.0) on a Linux Ubuntu system and that version works so I tried installing the same version of Firefox to...with wha…

Chrome msaR Firefox browsers

updated 4.3 years ago • amon

Because the reference file I used to generated the VCF file is HG19. So I cannot use the latest version of the ensembl DB. I checked the  Ensembl DB web site and find out the latest version for HG19 (GRCh37) is the archive...SNP/snp\_ref.cgi?rs=200322093) Does anyone know the reason? In addition, I notice in the latest version of the DB, it has a field called "<span style="line-heig…

R biomart MAF

updated 10.4 years ago • jz6002

when i install the package org.Hs.eg.db in R (version 4.0.5 ),i met some problem. can you give me some suggestion? Thankyou! >BiocManager::install("org.Hs.eg.db") 'getOption...replacement repositories: CRAN: https://mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.12 (BiocManager 1.30.15), R 4.0.5 (2021-03-31) Installing package(s) 'org.Hs.eg.db' installing…

AnnotationDbi org.Hs.eg

updated 4.5 years ago • 1065463017

Hi, I'm having trouble when using the xy2indices function of affy package. In version 1.40.0 of affy, one parameter for this function was nr (number of rows on the chip). In the version I'm currently using 1.48.0...but it was already the case in version 1.46.1), this parameter doesn't exist anymore and seems to be replaced by nc (number of columns on the chip). Moreover when...I'm trying to ind…

xy2indices affy

updated 10.2 years ago • VeloSand

arrays.I have problems in defining the universe and the selected genes though I referred to a number of documentations: My data is as follows: myd #str(myd) chr [1:22810] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at...ID used by your annotation package.\n For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).") univ } I tr…

Annotation GO ath1121501 probe Annotation GO ath1121501 probe

updated 13.1 years ago • Guest User

couldn't work out how to upload an attachment with it but would if I could. ---------- Output: Identifier logFC AveExpr t P.Value adj.P.Val B log.P.Value log.adj.P.Value Threshold Threshold_adj.P.Val pvaluecheck...lt;- eBayes(fit2_paired) finalresult_paired <- topTable(fit3_paired, adjust.method = "BH", number = Inf) setDT(finalresult_paired, keep.rownames ="Identifier") setD…

limmaGUI limma adj.p.value StatisticalMethod

updated 3.2 years ago • walkerrh95

I would like to create a data.frame with both ENSEMBL and ENTREZID gene identifiers for several species, including the human and the *Macaca fascicularis* genomes. I noticed that the latest EnsDb...object available (`AH100643` = ensemble version 106) for the human genome only contains ENTREZIDs for ~ 40% of the ENSEMBL gene identifiers. (See reproducible example...columns = "ENTREZID", …

AnnotationHub org.Hs.eg.db ensembldb

updated 3.4 years ago • sandmann.t

end of the program after a call to Rmpi::mpi.finalize() the problem does not occur with an older version of R (3.4.4) only the most recent 3.x versions as well as 4.x

Rmpi

updated 5.4 years ago • hstern2

Dear list, this seems like a trivial question, but I haven't been able to find a function to serve this particular need: I want to trim a variable number of bases off the end of a read, in the following manner: If the length of a read is x, trim y bases. If the length of a read is x...but I haven't been able to find a function to serve this particular need: I want to trim a variable number…

Biostrings

updated 9.8 years ago • knaxerova

div class="preformatted">Using the Win version of R 1.7.0 and Affy 1.2.14, I was able to modify the hist function to plot lines rather than numbers using a command like...hist(abatch, type="l", lty=1, lwd=2) Now with R 1.7.1beta and Affy 1.2.27, this doesn't replace the numbers with lines. I can sort of emulate the lines by cranking the number size down with cex=0.1, but I really prefer the l…

Microarray affy Microarray affy

updated 22.6 years ago • James W. MacDonald

the instructions in the GOStatsForUnsupportedOrganisms.pdf. We've rolled up expression to Ensembl identifiers, so I've used biomaRt to pull the evidence codes and identifiers thus: go_id Evidence gene_id 1 GO:0016567 IEA ENSG00000259662...5 GO:0005576 IEA ENSG00000261933 10 GO:0007049 IEA ENSG00000227268 but when I R version 2.13.0 (2011-04-13) Platform: x86_64-unknown…

GO affy GOstats biomaRt GO affy GOstats biomaRt

updated 13.3 years ago • wrighth

<div class="preformatted"> Dear list, I am having problems with the "spillover" method of the flowCore package. I am trying to compensate a flowset but everytime I tried to get the spillover matrix from my control data, I received the following error message: "Error in .local(x, ...) : subscript out of bounds" In my flowset I have 6 flowframes (in the following order: unstained cells, AP…

updated 15.8 years ago • Frederico Arnoldi

div class="preformatted"> Hello, I'm trying to use DEXSeq to identify alternative exon usage. Using DESeq I've identified ~200 differentially expressed genes in my gene set. I've basically...possible that something is wrong in my analysis? Regards, Philip -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base pac…

GO DEXSeq GO DEXSeq

updated 13.0 years ago • Guest User

div class="preformatted">All, I understand the concept of multiple probesets corresponding to one identifier. But what is the meaning of a probeset corresponding to multiple identifiers? And below, given that 220547_s_at...219666_at 64231 5 220547_s_at 414241 6 220547_s_at 439965 > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit…

biomaRt biomaRt

updated 13.6 years ago • Juliet Hannah

readBeadSummaryData(dataFile = dataFile) : Could not find a column called ProbeID to use as bead identifiers. Check your file and try changing the 'ProbeID' and/or 'skip' arguments. The error said " Could not find a column called...beadarray package suggest how to get over this? Thanks a lot! Allen [[alternative HTML version deleted]] </div

beadarray beadarray

updated 17.6 years ago • affy snp

mentioned exon belongs to multiple isoforms (in some cases to multiple genes), is there a way to identify exactly to which isoform (or gene) this exon belongs to? Thank you very much. Regards, Nirmala [[alternative HTML version

DEXSeq DEXSeq

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

Hi, I'm analysing RNA-seq data and I switched from edgeR to DESeq2 because most of my differentially expressed genes had an outlier sample, which was not an outlier in the entire dataset (judged by PCA and overall Cook's distance). My question is related to the criteria used by DESeq2 to count the number of replicates in my experiment. I have 3 experimental groups, A,B and C, each of them with…

deseq2 ruvseq cookscutoff covariates batch

updated 9.1 years ago • j.viana

<div class="preformatted">I have posted this problem earlier, but there was no response. Hence, I'm posting this again. I have installed R version 2.3.1, on Mac (OS 10.4.7, on an Intel CoreDuo iMac). When I try to install bioconductor -- following instructions, using biocLite...this problem earlier, but there was no response. Hence, I'm posting this again. I have installed R version 2.3.…

affy affy

updated 19.3 years ago • Debashis Bhattacharya

Error is following- Error in load(file = "WGCNA_module_part_1.RData") : bad restore file magic number (file may be corrupted) -- no data loaded In addition: Warning message: file ‘WGCNA_module_part_1.RData’ has magic number...libra' Use of save versions prior to 2 is deprecated

WGCNA

updated 4.6 years ago • abhisekdey061

genes_id_list' = genes), > + action = KEGGaction, nameSpaces = SOAPNameSpaces(version=1)) > xmlns: URI SOAP/KEGG is not absolute > xmlns: URI SOAP/KEGG is not absolute > character(0) >> >> There does seem

KEGGSOAP KEGGSOAP

updated 14.0 years ago • seth redmond

seem to be 2 categories of difference: (1) Some genes listed by Biocarta are absent from graphite's version (see ??? marks in the example below). (2) Because the native format nodes are annotated variously, it's necessary to do a node...s "PROTEIN LIST" gives _specific_ members of enzyme families, whereas graphite seems to replace EC numbers with all family members. However, I have trouble explai…

Transcription Pathways Leukemia graphite Transcription Pathways Leukemia graphite

updated 13.6 years ago • Hamid Bolouri

Hi, I couldn't find the external_gene_id attribute in the new biomaRt version. Is there any reason for that? Thanks a lot. D

biomaRt Ensembl Ensemblplants

updated 6.5 years ago • Didi

data. I have two other questions for you today ;-) The first question is about your new version of DESeq2 : - I found about 140 DEG when I used a previous version (v1.0.9) - Now I am using your new version v1.0.19 with exactly...FALSE in nbinomWaldTest, I find ~ 370 DEG. What are the other differences between the two versions ? (only outlier detection is reported in the NEWS file) …

DESeq2 DESeq2

updated 12.2 years ago • amandine.fournier@chu-lyon.fr

require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.18") ``` in R (version 4.3.0), I get the following error: ```r Error: Bioconductor version cannot be validated; no internet connection...ensuring internet connection, etc) have helped either. The documentation suggests that the version map can be found at [https://bioconductor.or…

Install

updated 2.1 years ago • Alexander

Aa credit loan customer care number /+9827075367///⑧⑨⑥②⓪⑨⑦⑤③④/ call meEnter the body of text here Code should be placed in three backticks as shown below...Aa credit loan customer care number /+9827075367///⑧⑨⑥②⓪⑨⑦⑤③④/ call meEnter the body of text here Code should be placed in three backticks as shown below ```r

cellxgenedp InteractiveComplexHeatmap hu6800probe lpNet MetID

updated 2.6 years ago • Hakp

m new to R and bioconductor. I cannot install some package, as they seem to be incompatible with the version of R I'm using (see below). I can't have the R updated at the moment. Is it possible to install older version of the packages

bioconductor

updated 9.5 years ago • lech

I am working on two colours microarray experiments and, from a set of 42000 genes, I would like to identify the differentially expressed ones. I have read several articles on this issue and most of them imply that the number...of differential expressed genes in such experiments should be a small number (compared to the whole set). Could anyone tell me why this is correct? What if I find half of …

Microarray Normalization Microarray Normalization

updated 19.6 years ago • Kimpel, Mark W

div class="preformatted">It is true I received a number of answers providing examples of data extraction from Ensembl. However, none of them extracts any identifier contained...UGUAAACAUCCUCGACUGGAAG) or in file "/hsa.gff" All the three above mentioned files contain the miRNA identifier and some other identifier that I do not know what it is. You may ask me why I haven't try to get all possib…

miRNA Biophysics Homo sapiens biomaRt PING miRNA Biophysics Homo sapiens biomaRt PING

updated 16.5 years ago • mauede@alice.it

Hello, I am trying to install DeSeq on my RStudio, but it is not working. Is it because of the version I have (3.6.2) or something else? Thanks for the help

deseq2

updated 5.5 years ago • enriqueza

stupid question, but I couldn undertand how to do that. I have a vector with a column with negative numbers(double). I want to change all negative to positive. I then made a function: ----------------------------- function(number){ if(number < 0){ number <- number...1 } return(number) } ----------------------------- then I run > bed[12] <- arruma(b…

updated 12.8 years ago • Guest User

gt; M <- 1:4 > g1 <- randomGraph(V, M, 0.2) > g1 A graphNEL graph with undirected edges Number of Nodes = 10 Number of Edges = 16 > plot(g1) crashed here! As you can see below, I recently installed R v2.11.1 on Windows Vista...The graphviz is version 2.20.3.1 (quite an old one but Rgraphviz specifically mentioned this version). Any ideas? > sessionInf…

graph Rgraphviz graph Rgraphviz

updated 15.6 years ago • Tae-Hoon Chung

will be highly appreciated. Here is my code and the result I got. Attached please find the package versions I'm using. Thank you all. Best, Ying >library(affy) >library(simpleaffy) >library(frma) >library(mouse4302frmavecs...Probe level linear model (PLMset) object size of arrays=1002x1002 cdf=Mouse430_2 (45101 probeset ids) number of samples=8 number of probesets=4…

convert frma convert frma

updated 14.2 years ago • Wang,Ying

biocLite() in the usual way. You will automatically get edgeR 2.4.6. In fact, you will get the version of any package that was part of Bioconductor release 2.9. If you want to run edgeR 2.4.6 in parallel with the current...On Tue, 5 Mar 2013, Zhuzhu Zhang wrote: > 4. Is there a place that I could download the older versions and manuals > of edgeR? I didn't find one on BioConduct…

edgeR edgeR

updated 12.8 years ago • Gordon Smyth

AffyBatch object size of arrays=1002x1002 features (8 kb) cdf=Mouse4302_Mm_ENTREZG (16395 affyids) number of samples=9 number of genes=16395 annotation=mouse4302mmentrezg notes= > data.norm <- gcrma(data, fast=FALSE, affinity.source...multiple of replacement length 3: In Yin[subset] = y0.adj : number of items to replace is not a multiple of replacement length 4: In Yin[subset] = …

probe gcrma probe gcrma

updated 17.0 years ago • Guido Hooiveld

and Genomics Clinical and Experimental Sciences Univ. of Southampton [[alternative HTML version deleted]] </div

Normalization Normalization

updated 11.8 years ago • Michael Breen

I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c genes.cc -o...genes.cc:100:9: error: use of undeclared identifier 'random_shuffle' random_shuffle( gene_vec.begin(), gene_vec.end(), rng ) ; ^ 1 error generat…

GOfuncR

updated 2.3 years ago • Marek Gierlinski

The following is a large text file I write few lines of it, I need to extract some genes from here according to my input please write a small script. I specified Input-output at the bottom of the post. This problem could seem very tough but in brief, I just want to recognize the associate gene id of one version from another, because online sites do not have the repository of this species. ``` S…

bash r bingo

updated 4.5 years ago • abhisekdey061