Bioconductor Forum

BPPARAM) 3: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, identifier = identifier) 2: lapply(all_expression_sets, virtualArrayBuildfData, collapse_fun = collapse_fun, identifier...virtualArray.Rnw' > > ################################################### > ### code chunk number 1: options > ###############################…

Microarray Annotation Preprocessing hgu133plus2 hgug4112a virtualArray Microarray hgug4112a

updated 11.5 years ago • Guest User

Dear all, I did a RNA-seq analysis two years ago (2011), using edgeR package (I do not remember the version). I was asked to analyze the data again, and now I am using edgeR_3.2.4. The comparison is between two groups. The "backbone...is pasted bellow), and I just changed it to adapt the package modifications. It turned out that the number of differentially expressed genes (FDR<0.05) in t…

edgeR edgeR

updated 12.3 years ago • Fernando Biase

but am unable to locate the answer. I am using R 2.7.2, Bioconductor 2.2 with oligo package version 1.4 and SNPchip 1.4. I am new to high throughput SNP analysis. My goal is to perform copy number / LOH analysis on tumor...to work on in SNPchip. How do I use oligo to generate an oligoSNPset class object? (genotypes + copy number). In a related 2nd question, I need to merge the oligoSNPset class …

SNP Cancer graph oligo SNPchip oligoClasses VanillaICE crlmm SNP Cancer graph oligo

updated 16.6 years ago • Min-Han Tan

I have access to 5' nascent RNA-seq data that captures transcription initiation information at basepair resolution. For those of you familiar, the data produced is similar to CAGE-seq/5' PRO-seq/GRO-cap/csRNA-seq. **PROBLEM:** I would like to compare a promoter in two different conditions and identify initiation sites that are differentially expressed/used between these two conditions. **BACKGR…

DESeq2 tpm Normalization

updated 4.3 years ago • Carlos

Hi, when I run IHW on our server it uses lots of computational resources (at least 20 cores). I can't seem to find any way to modify this in the call to `` ihw() ``. Is there a way to reduce the number of cores used by IHW? Thanks! Example code (from the IHW package) and session info: library(IHW) X <- runif(20000, min=0, max=2.5...I can't seem to find any way to modify …

IHW lpsymphony

updated 8.2 years ago • Charlotte Soneson

Execution halted I'm left with one chromosome to wrap up the analysis. Is it possible to identify region the function is giving issues for missingness? Is it due to large number of SNPs, or low number of SNPs, or high...gdsfmt_1.14.1 GWASTools_1.24.1 Biobase_2.38.0 BiocGenerics_0.24.0 R version 3.4.2 (2017-09-28) Thanking you in advance

genesis admixmap

updated 6.2 years ago • GENOMIC_region

<div class="preformatted">Hi, I have identified a set of genes that are differentially expressed between 2 experiments run in duplicates. The aim of the study is to identify genes and pathways differentially expressed between a wild type and a mutated cell line. I have used the affy package and the RMA function with quantile normalization. Because of the small number of replicates I have us…

affy LPE affy LPE

updated 22.4 years ago • Phguardiol@aol.com

This release contains data packages updated to public domain databases as of January 2005 and can be identified by a version number matching 1.7.x. Still Missing ========= The following packages are not yet available, but will be in the...repository here: http://www.bioconductor.org/data/metaData/html/ NOTE: Because we used the latest version of R to build the packages, you will see a warning …

updated 20.8 years ago • Seth Falcon

stringsAsFactors=FALSE) } # print the top 50 genes print(topTable(fit, adjust='fdr', number=5)) ## get significant gene list with FDR adjusted p.values less than 0.01 p.adj <- p.adjust(fit$p.value[,2]) sigGene.adj...how do I properly set up each pairwise comparison? thanks paolo -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: i386-…

updated 13.4 years ago • Guest User

<div class="preformatted">Hi: We are learning to use the marray suites of packages for our spotted array data analysis. I have encountered problem that I can not resolve. I wonder if someone can help me identify what I am doing wrong here. In this case I am creating a marrayRaw object from a .gpr file that only contains one array. My code looks like the following: …

GO marray GO marray

updated 22.1 years ago • Lin, Michael W.

that represents ~150 genomic regions of interest. I want to use the location of those regions to identify any overlap with gene CDS or Promoters within the yeast genome. There is a convenient function within the GenomicFeatures

GenomicFeatures GenomicRanges

updated 5.9 years ago • vanbelj

and TCR data are quite different . I want to make sure that if I can still use the DropletUtils to identify cells in 10X 5` TCR data. If can , how to perform , which functions shold I employ and which paramaters shouls I pay attentions

DropletUtils 10X 5` TCR single cells

updated 6.7 years ago • xingxd16

nbsp; I'm running PureCN (development version V1.11.8) on a new project for the first time, and some errors occur, one of which is: WARN [2018-06-20 13:37:46] Could not impute...F INFO [2018-06-20 13:37:46] Segmenting data... Error in xg[1, ] : incorrect number of dimensions Calls: runAbsoluteCN ... <Anonymous> -> .calculateMapping…

PureCN

updated 7.5 years ago • twtoal

The query to the BioMart webservice returned an invalid result. ## The number of columns in the result table does not equal the number of attributes in the query. ## Please report this on the support...site at http://support.bioconductor.org sessionInfo() # R version 4.0.0 (2020-04-24) # Platform: x86_64-w64-mingw32/x64 (64-bit) # Running under: Windows 7 x64 (…

biomart

updated 5.5 years ago • daniil.sarkisyan

and I am normalising using the NEQC function in the LIMMA package. I know there are traditionally a number of Illumina identifiers and I am concerned that I may have potentially been using the wrong ones, and I'm not sure whether...at all. After summarisation in Genome Studio, when looking at the 'Sample Probe Profile', the main identifiers that come up (and which I have used in LIMMA) are 'PRO…

Microarray Annotation probe limma Microarray Annotation probe limma

updated 12.4 years ago • William D'Avigdor

div class="preformatted">I plan on using DESeq downstream of CCAT identified peaks on 5 tumor and 5 normal samples and I was unsure of how to best create a unified list of peaks and corresponding

ChIPSeq chipseq DESeq ChIPSeq chipseq DESeq

updated 11.6 years ago • Guest User

Hello, I am new to EdgeR and I am working on processing some proteomics data to identify DEPs between two samples (sample vs control, both in triplicate). I've been working through the EdgeR documentation...BCV is something like 6% (not sure if this is good). I've been testing different approaches to identify DEPs and I am curious how I should compare results between QLF and LRT tests. My…

edgeR

updated 2.8 years ago • Tanner

nbsp; I'm trying to work out a function or find a package that lets me normalize omics data to cell number.  So after counting cells for a certain condition and running the omics experiment, I would use the mean cell count...this would be? Perhaps there's already a package available that allows me to specify the cell count number?  Thank you

normalization normalize cell

updated 7.5 years ago • bhgyu

together. If so, I thought to use the unstranded data for my DGE analysis to reach the final number of 4 replicates per stage. I mapped the raw reads to the genome using TOPHAT (v2.0.9) (fr- unstranded for unstranded data...htseq-count on the stranded data selecting the option -s no and in this way I got a very similar number of total counts between the unstranded and stranded data, around 4-5M …

Normalization DESeq Normalization DESeq

updated 11.8 years ago • Federico Gaiti

I'd like to use BioNet to identify high-scoring subnetworks in my data. The tutorial clearly explains how to identify the _top_ scoring subnetwork...interactome) subnet <- rmSelfLoops(subnet) subnet A graphNEL graph with undirected edges Number of Nodes = 2559 Number of Edges = 7788 fb <- fitBumModel(pval, plot=FALSE) scores <- scoreNodes(subnet, fb, fdr=0.001) m…

bionet network

updated 9.5 years ago • enricoferrero

<div class="preformatted">Dear list, I am trying to generate a list of probes that are differentially regulated after stimulation in cells with a gene knockdown vs. the wildtype controls. I generated two constrasts and looked at the overlap with a Venn diagram. It looks like this: diff_con(2288(3069)1010)diff_kd I am interested in whatÂ´s going on in response to the gene knockdown - like…

GO GO

updated 15.1 years ago • Moritz Kebschull

names with an asterisk? For example all of my gene IDs always start with TgEST followed by various numbers, can I type TgEST* to identify all genes and then * for all controls? All of my controls have different sorts of names. Do...toxo/ Tel 01223 33 33 31(office) or 01223 33 33 29 (lab) [[alternative HTML version deleted]]</div

updated 21.4 years ago • Elizabeth Brooke-Powell

my coding and any help would be greatly appreciated. Below is my current code: nr=dim(fileName)[1] #number of rows count=0 for(i in 1:nr) { for (j in 1:nr) { if(fileName$Individual[i]==fileName$Individual[j] & i != j) #look for a pair in the column...In the matrix (fileName), first it searches for a pair in column: Individual, and once identified it permutes another column (Group). I w…

PROcess PROcess

updated 14.1 years ago • Kripa R

Hello, I have a list of refseq numbers each with a KPRM value before and after a transformation of cells in an attempt to make immoralised cells. I need to

differential gene expression r commander

updated 9.7 years ago • milliesteward23

me to minimize the contribution of genetics and environmental variability, focusing instead on identifying genes with high variability due to stochasticity/noise. My approach involves: 1. Using DESeq2 for differential...groups) and standard deviation (SD) as measuring vertical differences (within groups), aiming to identify genes that are changing due to biological factors rather than tech…

DESeq2

updated 16 months ago • DL

Hi, I am still trying to get beadarray's readIllumina() working with recently acquired data from HT-12 v4 beadchips and using a sample sheet. No matter what I was trying in that sample sheet, I always got: <pre> Error in analyseDirectory(dir = x, sectionNames = as.character(dirs[[x]]), : Directory does not exist.</pre> So I started to debug the readIllumina() function and not…

beadarray bug illumina human ht-12 v4 illumina beadchip

updated 8.6 years ago • S. K.

for annotation. I am trying to build the gene length database by myself, given that the current version of goseq does not support the mm10 build. 1, Cufflinks seems ignored the original gene identifier that comes with the...and make its own, but they do keep the gene name in its record, so I will just take gene name as identifier in my process. I have already used the gene names for building th…

Annotation GO PROcess goseq Annotation GO PROcess goseq

updated 12.5 years ago • Guest User

What is the best way to convert uniprot accessions to entrez gene identifiers? What is the best way to reverse the map org.Hs.eg.db::org.Hs.egUNIPROT ? Is there any better approach (a pity there

org.hs.eg.db uniprot accessions entrez gene identifiers

updated 10.3 years ago • Aditya

Good Morning, I need some advice on some gene expression research. I have datasets which are downloaded from GEO and customized into MS excel. I need to identify the common genes across all the datasets. I've been reading that there is a way I can use R/Bioconductor in order to simply...research. I have datasets which are downloaded from GEO and customized into MS excel. I need to identify the c…

datasets genes gene expression

updated 10.3 years ago • vavecilla

if I need to use cghMCR to identify minimum common regions I would need to construct CNA data object with call. Is there any alternative to this rather...list object and is a better alternative > to > the MCR approach. If you read the latest version of cghMCR, there is a > section showing the steps to take. > > If you would want to make a DNAcopy object off a se…

PROcess DNAcopy cghMCR PROcess DNAcopy cghMCR

updated 14.2 years ago • viritha kaza

Hi, there is a missing GO id in hgu133a GO.xml <annbuilder:entry describ="Gene Ontology identifier" id=""> <annbuilder:item name="GO2AFFY" value="203787_at"></annbuilder:item> <annbuilder:item name="GO2AFFY" value="210829_s_at

GO hgu133a hgu133b GO hgu133a hgu133b

updated 23.1 years ago • Ken Stickler

to compare one gene (from the host) to all the genes (from the pathogen) at a time, and identifying significantly correlated genes based on FDR values. Given that large number of comparisons is done, with large...number of correlations, I was wondering about the possibility of high correlations surfacing even with random ordering...questions/5750/look-and-you-shall-find-a-corre…

edger rna-seq correlation

updated 9.2 years ago • jhj89

Hi, is it possible to optimise (speed up) dispersion estimation step in DEXSeq (1.34.0) analysis when working with large number of samples? I noticed that almost 80-90% of the analysis time is actually dispersion estimation, which in my last run with...optimise (speed up) dispersion estimation step in DEXSeq (1.34.0) analysis when working with large number of samples? I noticed that almost 80-9…

DEXSeq estimateDispersions

updated 5.5 years ago • aleksandar.baburski.g

div class="preformatted">Dear group, I'm trying to detect copy number variations with the cn.MOPS package. I have eight different samples (coming from different individuals re-sequenced...default parameters. However, when I run the algorithm it detects some CNV regions for which the copy number is 2 for all the individuals. Does anyone have an explanation for this result? I paste you here the…

Coverage cn.mops Coverage cn.mops

updated 13.0 years ago • lpascual

div class="preformatted">Hi The golub dataset has identifiers which I can only assume are based on GenBank/EMBL accession numbers (Eg M71243_f_at, U29175_at etc). I want to enrich...the annotation for this data set by mapping these identifiers to GO terms, KEGG pathways etc but I can't figure out how to do it using bioconductor. Can anyone give me a few tips

Annotation Pathways GO Annotation Pathways GO

updated 20.8 years ago • michael watson IAH-C

gt; Hello Gordon, > > Thanks a lot for your reply. > > How can I upgrade to the latest version of edge R? I have checked on the > list and it looks like i need version 2.99.3. However, the one you provide > at http://www.bioconductor.org...packages/2.10/bioc/html/edgeR.html is > edgeR_2.6.12. How can I get the needed version? > > Than…

edgeR edgeR

updated 13.2 years ago • Gordon Smyth

the SamSPECTRAL algorithm, at the beginning of the resulting vector containing the assigned cluster-number for each datapoint, SamSPECTRAL seems to count up to the number of clusters one time. Let me explain by using this example...starts to count from 8 to 16 (the number of clusters is 16). This behaviour is consistent and reproducible on all my datasets. It is also present, when there is...more…

samspectral

updated 10.5 years ago • benediktbrink

to load an FCS file containing multiple data segments, and am trying to automate the process but the number of datasets varies - I would like to be able to automatically get the number of data segments to then use a loop to store...them all. There seems to be some built-in function for quickly checking the number of segments, as if I use ```read.FCS``` without specifying a dataset, it instantly r…

flowCore

updated 4.7 years ago • mark.holmes

I want to be able to find the minimum and maximum intensity levels in that object and in some number of pixels around the max and min. I would also like to know which pixels these are. I could possibly write my own function...image after segmentation to find the pixels where 0 is next to a non 0 value and then from that identify the max and min intensity values in the grayscale image. Thank yo…

EBImage EBImage

updated 12.7 years ago • Kevin

F 22 S7 1 P NR 28 M 34 S8 2 P R 47 M 24 ``` Essentially, these are hundreds of sample. I aim to identify differentially expressed genes in DR vs DNR. However, I also need to control for covariates. Therefore what I am doing

RNASeqData DESeq2

updated 2.4 years ago • Abhishek Singh

Dear All, I run the following code with my dataset res in order to transfer REFSEQ identifiers into ENTREZIDs. It was successful. However, about 30,000 of REFSEQ IDs like XP_047XXXXXX (for example, XP_047283139

org.Hs.eg.db

updated 3.2 years ago • mengs

element is a list with one logical vector per sample. These vectors are all the same length as the number of peaks in the merged set. The logical values indicate if the merged peak overlapped with a peak in the original peakset...Site vectors are also accepted as parameters to dba.plotHeatmap() and dba.plotPCA() to identify a subset of global sites (e.g. only the sites identified in one of the or…

DiffBind DiffBind

updated 11.5 years ago • Rory Stark

S0,S1, and S3. I am creating the contrasts and doing the fit function but its giving the error ( Number of rows of contrast matrix must match number of coefficients in fit) ``` > contrast.matrix <- makeContrasts( + S1_vs_S0...lt;- limma::contrasts.fit(fit, contrast.matrix) Error in limma::contrasts.fit(fit, contrast.matrix) : Number of rows of contrast matrix must ma…

limma

updated 19 months ago • zzrammal

_cell\_names=FALSE), there are 4 isolated clusters which not have connections with other clusters number.  Is there any parameter wrong in my functions?   (2) Next, I intend to use the TSCANorder() function to get the...TSCANorder(mclustobj = lpsmclust, MSTorder = NULL, orderonly = T, flip = F, listbranch = F) But the number of elements in lpsorder is 10404 , however,…

TSCAN software error

updated 8.5 years ago • yancychy

div class="preformatted"> Sean, Thanks! The gold is to identify copy number variation from normal human samples. I have tried CBS, cghFLasso (http://biostatistics.oxfordjournals.org...wrote: > > > > Hi All, > > I have a question about analyzing aCGH data with huge number of > > probes on a single chromosome. > > We have …

aCGH aCGH aCGH aCGH

updated 17.7 years ago • pingzhao Hu

<div class="preformatted">Hi Jim et. al, I am attempting to analyze data from humans exposed to arsenic in vivo from an affymetrix Human Gene 1.0 ST Array. I have generated differentially expressed genes lists using LIMMA and an ANOVA. I am encountering a high number of control probes as top genes in both lists and am not sure if I should be ignoring this information, removing it, or util…

probe limma Category probe limma Category

updated 13.7 years ago • Alexandra Muñoz

I am running DESeq2 to find associations between microbiome abundance and gene expression. The results include accession numbers that look valid but do not appear in the reference that was used when calculating the gene counts and according to the ensembl ID converter were never valid ensembl IDs implying the problem is not that I used an old reference. This is the code that is running DEseq2…

deseq2

updated 6.0 years ago • JGibbons1

<div class="preformatted">Transcripts not expressed in control but which have high expression in treatment theoretically have an infinite fold-change. Preprossesing algorithms will provide numbers for fold-change for these genes, but to do this there seems to be an assumption that all genes are expressed to some small...in treatment theoretically have an infinite fold-change. Preprossesing …

GO Preprocessing GO Preprocessing

updated 16.5 years ago • Matthew McCormack

I'm currently working on genomic data which contains chromosome start and end position. I want to identify the genomic region which overlap to another region and collapse them into new genomic region. Although I can identify...745, ")) The value in subjecthit column should not in queryhit column. For example, in row number 2 ,queryhit colummn equal to 2 and subjecthits column equal to…

GenomicRanges r

updated 6.5 years ago • naktang1

div class="preformatted">Hi, Is there a maximum number of sequence files (chromosomes or contigs in my case) that can be fed to the forgeBSgenomeDataPkg() function? I am trying...www.stowers.org Tel: 816-926-4071 Cell: 816-726-8419 Fax: 816-926-2018 [[alternative HTML version deleted]] </div

BSgenome BSgenome genomes BSgenome BSgenome genomes

updated 12.7 years ago • Marco Blanchette

of the mailing list, but still cannot find an exact answer to my problem. (1) Question: Can a large number of CEL files cause an overflow for the function ReadAffy() in the affy packages? Is there any way to fix this? Other options...but when I moved on to 2,035 CEL files, it failed and kept showing the error message below. The number of rows for the CEL file is roughly 50k. On the bright side, …

affy affy

updated 17.4 years ago • Hailong Cui

I am using DESeq2 to identify genes that are differentially expressed in mammalian tissue (n = 3 subjects) in response to 8 different treatments...Treat. However, after extracting results for my comparisons of interest, I noticed that the number of DEGs was not consistent with the distances between samples on the PCA plot. I know that the gene counts used for PCA

DifferentialExpression DESeq2 contrasts

updated 4.5 years ago • Jane

Hi all, I'm using edgeR for DEG analysis and have run into a snag with my filtering approach. I have an experimental design wherein individuals from two different populations were treated with a drug or left untreated. This is not a repeated measures, and replicates are not shared between treated and untreated for a populations. The populations are A and B, and the treatments are T and U (untrea…

edger filtering

updated 7.0 years ago • rproendo

Hi, I’m running a project concerning copy number variation analysis. To run the analysis, I need to visualize the copy number data that I have. The data I have is in VCF files...fileDate=20190921 ##source=CNVkit v0.9.1.dev0 ##INFO= <id=ciend,number=2,type=integer,description="confidence around="" end="" for="" imprecise="" interval="" variants"=""> #…

copynumber plot visualization NGS gene

updated 5.0 years ago • sijing.gsj

fullXmlQuery, : The query to the BioMart webservice returned an invalid result. The number of columns in the result table does not equal the number of attributes in the query. Please report this on the support...Am I doing something wrong here? here's the results of sessionInfo() ```r R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monter…

biomaRt

updated 3.3 years ago • noah.reid

<div class="preformatted"> I'm in search of copy number analysis implementation that would fit for Hadoop/Mapreduce paradigm; I appreciate if anyone has used/experienced with copy number analysis that can be used with Hadoop/Mapreduce and point me to those. Hadoop is a software framework on Linux that allows...div class="preformatted"> I'm in search of copy number analysis implementatio…

updated 13.7 years ago • mcoyne@boninc.com

by Agilent. After mapping, I want to do DEG analysis utilizing DESeq, and I found the gene number would affect the results given by DESeq. So my question is whether DESeq compatible with limited genes (83 candidate...candidate genes' RNA-seq? or, for my project, I could just calculate RPKM value for each gene, and identify DEGs simply by fold change > 2? Thank you! Sincerely, …

Sequencing DESeq Sequencing DESeq

updated 12.3 years ago • 邵建明

and the beadarray package. It seems they are all giving pairwise plots. When I have had a large number of Affy arrays, I have had success with the MAplot function in affyPLM because I believe it takes the median of all arrays...general function similar to this that I can use on a matrix. Thanks! Juliet > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-unknown-linux-gnu (64…

affy affyPLM beadarray lumi affy affyPLM beadarray lumi

updated 14.1 years ago • Juliet Hannah

edges, e.g. > kegg[["ErbB signaling pathway"]] "ErbB signaling pathway" pathway from KEGG Number of nodes = 87 Number of edges = 0 Type of identifiers = native Retrieved on = 2011-05-05 Whereas the KGML for the same pathway...in KEGG also, e.g. kegg[["Spliceosome"]]. I am _not_ talking about those. > sessionInfo() R version 2.15.0 (2012-03-30) Platform:…

graphite graphite

updated 13.6 years ago • Hamid Bolouri

paper PMID 22024983 (https://www.ncbi.nlm.nih.gov/pubmed/22028943) they have used ANOVA method to identify the significant genes,Now i am  trying to compare their results with Limma package but i am not getting any single

limma microarray

updated 8.9 years ago • mathavanbioinfo