Bioconductor Forum

Hello there. I would like to identify the cell line-independent differentially expressed genes in a time series experiment, i.e. those genes that respond...resTC[order(resTC$padj),], 4) ``` ``` #sessionInfo just in case > sessionInfo() R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Sierra 10.12.6 locale: [1] en_US.UTF

deseq2

updated 6.3 years ago • jhnwphillips

div class="preformatted">After languishing for about 9 months, I have finished a new version of annaffy. It represents almost a complete rewrite including: - separation of data retrieval and HTML/text generation...user data - a vignette (annaffy is now fully Bioconductor compliant) - updated for use with the version 1.2.6 affy data packages - more robust and expandable data structures - perva…

GO affy GO affy

updated 22.5 years ago • Colin A. Smith

use multiple cores when appropriate, much like mclapply in the parallel package. Like mclapply they identify and utilize all available cores by default. On a multi-user system that is frowned on. The tallyVariants argument...list includes BPPARAM, I learned how to use that to specify the number of cores used (see code below). The help for summarizeOverlaps says "control parallel evaluation usin…

VariantTools BiocParallel GenomicAlignments VariantTools BiocParallel GenomicAlignments

updated 11.5 years ago • Guest User

nbsp; title: wgEncodeCshlLongRnaSeqHelas3CellPapGeneGencV7   reason: bad restore file magic number (file may be corrupted) -- no data loaded In addition: Warning message: file ‘1376’ has magic number 'chr16'   Use of save versions...prior to 2 is deprecated <pre> sessionInfo()</pre> R version 3.3.2 (2016-10-31) Platform: x86\_64-apple-darwin13.4.0 (64…

annotationhub

updated 9.0 years ago • jason.serviss

is actually simple: How can I manage to create several `DoparParam()` objects, each with a different number of registered cores? See below for what I tried. In a nutshell, it seems I can only have one `DoparParam()` object, because...I run `registerDoParallel()` existing objects will be overwritten in terms of number of registred cores. Why is that important? Say I need one DoparParam with just …

BiocParallel

updated 17 months ago • ATpoint

<div class="preformatted">Hi, There are 292 pathways according to pathway2gene, but there are 390 pathways according to pathway2name. I'm wondering why these two numbers are not the same. > library(KEGG.db) > pathway2gene=dbGetQuery(KEGG_dbconn(), "SELECT * FROM pathway2gene") > > species=unique(substr(unique(pathway2gene$pathway_id),1,3)) > species [1]…

Pathways Pathways

updated 14.2 years ago • Peng Yu

<div class="preformatted">Hi, Here is my question and I hope it fits into the BioC support group (!): I have one cell line A with a deficient gene and another one B with the corrected gene (same cell line indeed with gene transfered). I have some Xpts conducted under normal cell culture conditions and some others in which I have added a stressing agent - some at 10 nM and some others at 10…

DOSE DOSE

updated 22.6 years ago • Phguardiol@aol.com

install DESeq2 for R 3.1.3, but it is throwing an error : package ‘DESeq2’ is not available (for R version 3.1.3) I know R is updated tp 3.3 and above , is there any way via which can install the libraries on R 3.1.3 version? Any

R bioconductor deseq2

updated 9.3 years ago • minie

conditions (cond2) each, 3 time-points and each 3 replicates. Can DESeq2 handle this low sample number and replicates as well, and give me DEGs for cond1 and time, while cond2 should be constrained to not be differentially...expressed? Is there a lowest number of samples limit? Thank you

DESeq2

updated 2.5 years ago • Rockbar

trying to pre-process (bg correction, quantile normalization, summarization) the readings in a large number (~1,000s) of large microarray chips (~10^6 probes). As far as I can tell, pre-processing functions in most packages will load...created in (b). Summarize to probeset, gene, exon, junction level using your favorite version of preprocessCore::subColSummarize. -- Guilherme V. Rocha gvr…

Normalization probe preprocessCore Normalization probe preprocessCore

updated 11.8 years ago • Guilherme Rocha

edgeR via bioconductor on June 2012 and I used edgeR produce some data. Now I want to known which version of edgeR that I once used. Does anybody know how to get this? I am not familiar R, and I also tried the edgeR download page

edgeR edgeR

updated 12.9 years ago • Guest User

gt;> Tel: +44(0)1273678559 >> >> > sessionInfo() >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_GB.UTF-8/en_GB.UTF...with mRNA data from Affy 'drosophila2' arrays and miRNA data from Affy 'mirna3' arrays. I have identified …

miRNA drosophila2 probe affy convert affycoretools microRNA miRNA drosophila2 probe affy

updated 12.7 years ago • Fiona

I would like to know if is possible to filter out ranges by the number of probes within the range.   thank you very much

probe ranges

updated 8.8 years ago • julrodr80

to run pathview with expression data from potato RNAseq. My RNAseq was originally mapped on PGSC identifiers which I am able to convert into NCBI GeneID (Entrez) identifiers using gprofiler (https://biit.cs.ut.ee/gprofiler...the following in R: ```r #Read table in correct format. First column is read as character, not numbers. library(readr) pathviewdata <- read_csv("pathviewdata.csv…

annotation_package not_available_in_BioConductor pathview

updated 3.8 years ago • bertranbio

To: bioconductor@stat.math.ethz.ch > Subject: [BioC] limma and Rank Products: comparison of the number of > results > Message-ID: <4B7BF8E9.5050105@cnb.csic.es> > Content-Type: text/plain; charset=ISO-8859-1; format...with > limma) and I'd like to know your experience when using both methods > regarding the number of results. > …

Cancer limma Cancer limma

updated 15.8 years ago • Aedin Culhane

Hi, This question is about RNAseq analysis in `EdgeR` to identify common and specific differentially expressed genes. I have 3 different Donor's in-vitro cultured tissue with two...Hi, This question is about RNAseq analysis in `EdgeR` to identify common and specific differentially expressed genes. I have 3 different Donor's in-vitro cultured tissue with two different infection status, one with …

R edgeR RNASeq

updated 2.4 years ago • mohammedtoufiq91

Ct"]]], ncol = n.data[i]) : data length [26994] is not a sub-multiple or multiple of the number of rows [750] 2: In matrix(sample[, column.info[["flag"]]], ncol = n.data[i]) : data length [26994] is not a sub-multiple or multiple of...number of rows [750] The first odd thing here is that my file has 29448 rows, not the 26994 quoted in the error (which turns out to...Ct"]]], ncol = n.data[i])…

miRNA miRNA

updated 13.0 years ago • Guest User

<div class="preformatted">Hi All, Why don't the numbers from summary(hgu95av2probe):199084 and length(pbn): 201800 don't match?!! There are more sequences than probe names?! I am...div class="preformatted">Hi All, Why don't the numbers from summary(hgu95av2probe):199084 and length(pbn): 201800 don't match?!! There are more sequences than probe names?! I

probe probe

updated 20.7 years ago • hrishikesh deshmukh

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regutools

updated 2.6 years ago • RANU

or it returns an error).  Nor can I use the function pm() because the probe to probeset id numbers are lost.  That is, with pm() the row identifiers turn into probe numbers. but with the function probes() i still get 1007

u133a normalization rma affy

updated 8.9 years ago • jxd_84

all, I'm processing some new IlluminaHumanMethylationEPIC arrays but I obtained different reading number of SNPs (nSNPsRead) in the IDAT files, 1051815, compared to the ones I've always usually got from IlluminaHumanMethylationEPIC...I have performed these tests for a single file because then creating the MethylSets I get a smaller number of probes, 866091, compared to what I always got and t…

illuminaio illuminahumanmethylationepicmanifest minfi

updated 7.9 years ago • Giovanni Calice

specifically limmaCtData to look for differential expression between groups, always having the same number of replicates. However, I currently have a dataset of several groups with 3 replicates and 1 group with 2 replicates...As far as I can tell, limmaCtData expects the number of replicates to be the same between groups (i.e. there is only one 'ndups' parameter). Has anyone else encountered t…

HTqPCR HTqPCR

updated 13.4 years ago • Fletez-Brant, Christopher NIH/VRC [C]

the upstream region to 5kb in case TP53 motif binding sites are particularly distant, but then the numbers of targets identified for TP53 and MYC are 12 and 7009 respectively. Can anyone spot an obvious mistake?  Or am I...print( length( unique(MYC.targets$gene_id[!is.na(MYC.targets$gene_id)] ) ) )</pre> --- R version 3.2.2 (2015-08-14) Platform: x86\_64-apple-darwin13.4.0 (6…

motifdb JASPAR transcription factor binding site

updated 10.1 years ago • Lisa Hopcroft

gt; gal <- readGAL() > layout <- getLayout(gal) Error in getLayout.default(gal) : number of grid columns is not 4 the final line in my GAL file looks like this: 1 105 215 Pro25G (+)Pro25G-03 1 pos Pro25G NA Im stuck

limma limma

updated 21.2 years ago • Morten

Hello, I have been using exomeCopy with no problem; however I was wondering if anyone has any insight about setting the possible copy number while running the exomeCopy function to get CNVs? I have trid both S=1:4 or 1:6 but I'm not sure if there is a general rule for...with no problem; however I was wondering if anyone has any insight about setting the possible copy number while running the exo…

cnv exomecopy

updated 10.0 years ago • cafelumiere12

Dear users, Instead of counts (non-negative integers) required by DeSeq2, I have negative numbers and fractions, and I need to use DeSeq's statistics to find out significantly up/down genes. Since for my data, min=-10...Dear users, Instead of counts (non-negative integers) required by DeSeq2, I have negative numbers and fractions, and I need to use DeSeq's statistics to find out significantl…

deseq2 logfoldchange

updated 9.1 years ago • rraadd_8

Hello, after using DESeq2 to analyze my dataset, I called the following code to count the number of genes with adj pvalue<0.05. However, when I export the data, the number of genes with adj pvalue<0.05 in the spreadsheet

DESeq2

updated 4.6 years ago • GlycineMax

I am surprised that `` bplapply() `` takes a few seconds to detect the number of available cores, while `` multicoreWorkers() `` or `` MulticoreParam() `` are fast when they run by themselves: <pre> > system.time...I am surprised that `` bplapply() `` takes a few seconds to detect the number of available cores, while `` multicoreWorkers() `` or `` MulticoreParam() `` are fast when …

biocparallel

updated 8.1 years ago • Charles Plessy

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hu6800probe lpNet

updated 2.6 years ago • Customer

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hu6800probe regutools lpNet cellxgenedp

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GRaNIE hu6800probe lpNet MetID regutools

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hu6800probe lpNet cellxgenedp

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BP4RNAseq RNAdecay LinkHD

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hu6800probe

updated 2.6 years ago • Chulu

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hu6800probe lpNet cellxgenedp

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lpNet

updated 2.6 years ago • Parbin

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ProstateCancerData

updated 2.6 years ago • Parbin

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hu6800probe

updated 2.6 years ago • Parbin

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cellxgenedp

updated 2.6 years ago • Customer

extracted up and down-regulated  genes from each comparisons using topTable, beside also identified the total number of up and down-regulated genes from each comparisons using summary(decideTests(fit2)) but I am...facing problem to identify/extract common genes that are DE in each of comparisons. Therefore, It is my kind request to all of you, please provides

limma bioconductor affymetrix microarrays R

updated 8.9 years ago • rkp

I'm using DEXSeq for the analysis of 16 human tissues. I'm trying to identify exons that are differentially expressed in one tissue against all other tissues and eventually trying to identify...expressed against all other tissues or again only one of them? how can I know through the numbers? I examined the intermediate results for the dxd object but what I found are columns for all the samples ve…

dexseq alternative splicing exon skipping

updated 10.7 years ago • ebadr

div class="preformatted">Hi, I want to create plots like the number of exons per gene in a list of genes, and the lengt of transcripts. My first choice would be to use R/Bioconductor and gtf...rank inference cannot accomodate trans-splicing. Appreaciate any suggestions! > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C attached …

Genetics TranscriptDb GenomicFeatures

updated 11.3 years ago • Jon Bråte

general explanation of variance adjustment, what it does and why? Additionally, when I add the batch number to the plate list and ask the program to do a variance adjust by batch, we get the following error: > x <- configure(x, + descripFile...not a multiple of shorter object length The error is not in the platelist file because the program identifies the different …

Normalization Normalization

updated 16.1 years ago • Baranes-Bachar, Keren NIH/NCI [V]

it is my first time posting here. Background: I need to compare genes across 3 tissue types to identify whether there is any difference in expression. I have created my DSEQ object in R from : 1. A gene:subject matrix - with...I have carried out the VST transformation and plotPCA. **So, to my current issue:** I need to identify which genes have the same or statistically similar expression …

DESeq2

updated 21 months ago • James Aiden

matrix annotated with Entrez IDs can be used directly. Thank you, Wendy [[alternative HTML version deleted]] </div

probe GSVA probe GSVA

updated 14.1 years ago • Wendy Qiao

<div class="preformatted">Thank you, Jim. One more question. The eBayes step adjusts the variance across genes. Since there is already a good estimate for the variance due to the large number of samples does the eBayes step shrink the variance even further? Thank you, Giovanni On Tue, Apr 29, 2014 at 9:20 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Giovanni, &g…

updated 11.6 years ago • Giovanni Bucci

Hi, I am trying to identify my DEG from the following code. However, my decide test summary results are different from the one written as csv...Hi, I am trying to identify my DEG from the following code. However, my decide test summary results are different from the one written as csv file, i.e. different number of up and downregulated genes obtained. Please explain the difference. ``` #Fit line…

edgeR voom decidetests DEG

updated 2.7 years ago • Ankita

Hi all! The total number of exon for the ZEB2 gene is greater than what has been reported in literature. DEXSeq shows 106 Exons since it should

DEXSeq exon

updated 3.7 years ago • jochen

differential expression across the conditions. Will this approach be valid? What is the minimum number of genes required by the statistical model implemented in DESeq? I apologize if the question are too naive. Thank you

RNASeq RNASeq

updated 13.8 years ago • vladimir mashanov

based on how they clustered. However, I am interested to find out further: 1) the total number of genes in each and then average number of genes from all 6 files? 2) conserved / non-conserved regions in exomes with respect

whole exome sequence R bioconductor exome

updated 8.8 years ago • bioinf

12:11 PM To: Federico Gaiti Cc: Steve Lianoglou; bioconductor@r-project.org Subject: Re: [BioC] Low number of replicates DESeq Then I would recommend the multifactorial design, as it's the best you can do without stranded...Lianoglou; bioconductor@r-project.org<mailto:bioconductor@r-project.org> Subject: RE: [BioC] Low number of replicates DESeq Hi Federico, Yes, Simon is right. Please i…

Transcription GO DESeq2 Transcription GO DESeq2

updated 11.8 years ago • Federico Gaiti

I dont know any other alternative as fast as longestConsecutive() but it has been depreceated in version 2.72 (Bioconductor version 3.19). I wonder why it has been depreceated and not replaced? Is there any better alternative

Biostrings

updated 18 months ago • Ali Osman

div class="preformatted">does anyone know why R packages versions do no follow the sources versions in the repositories? examples: *** siggenes "2.4.1" sma "2.4.1" spatial "2.5.0" splines

updated 18.5 years ago • D.Enrique ESCOBAR ESPINOZA

libraries amplified from single cells using the SMART protocol. Each sample required different numbers of PCR-cycles to get enough cDNA for library prep, and the quality of the cDNA was also variable (i.e. read length distribution...t know these things yet, it is hard to say whether we have replicates or not, but we hope to also identify differetially expressed genes between the differen…

normalization rna-seq deseq2 edger smart

updated 10.7 years ago • Jon Bråte

div class="preformatted">Hi all, I am getting a strange total number of affyids when importing data from MoGene arrays. The Affymetrix specifications say: Estimated Number of Genes: 28...5,222 Plus some hybridization Probes, Background Probes and Poly-A Control, but they don't give the numbers. Basically in total from the specified numbers, there should be 35399 affyids. However when I'm re…

updated 15.8 years ago • marek piatek BI

htmlTable", "ggplot2", "tidyverse", "reshape", "dplyr", "jsonlite", "xml2", "biomaRt"), ask = FALSE, version = "3.10")' ``` I understand that a specific Bioconductor release version should imply that a specific version of each bioconductor...constrained? Or running this installation script now and in 6 months result in differnet package versions being installed? Thanks! Yannick

reproducibility versions installing base-r

updated 5.7 years ago • Yannick Wurm

Hi, I have a question which is especially addressed to the authors of the "BiocParallel" package: In the vignette "Introduction to BiocParallel", you state (at the top of page 13): > Create a SnowParam instance with the number of nodes equal to the size of the MPI universe minus 1 (let one node dispatch jobs to workers) [...] The corresponding code starts...to BiocParallel", you s…

BiocParallel

updated 5.8 years ago • Homer

Hi, I'm writing just to ask if someone knows the latest version of R compatible with BSgenome. When I try to install the latest available version of R, version 3.3.1, i get: package ‘BSgenome...is not available (for R version 3.3.1) (the same with GenomicFeatures, and probably related genome manipulation packages) Should I install 3.2.5...or is it compatible with R version 3.3.0? Regard…

bsgenome

updated 9.4 years ago • pj dias

i.e. *Clostridium beijerinckii* NCIMB 8052. I have read paper and information about it that it is a number to identify genes specifically but I am struggling with finding the source where to look for it. Thanks a lot

annotation

updated 6.2 years ago • mnazir

I want to install DESeq2 version 1.16.1. My Bioconductor version is 3.10. I tried to install it by downloading this version from: https://bioconductor.statistik.tu...R CMD INSTALL DESeq2_1.16.1.tgz * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *binary* package ‘DESeq2’ ... * DONE (DESeq2) but getting this error…

deseq2 software error

updated 5.9 years ago • joshianu2018