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GRaNIE MetID

updated 2.6 years ago • RANU

div class="preformatted">Hi, Jean, Could you send me a copy of the test version of gcrma too? I am having problems with the released version--memory problem. I have tried unsuccessfully to run gcrma...on the data from 60 RG-U34a chips (all versions of R and bioconductor packages); but it was OK for data from 30 chips. Thank you. The runs were on a PC with intel 3.06 GHz...athena.biostat.jhsp…

gcrma gcrma

updated 21.9 years ago • Puhong Gao

Now preprocessing raw data of GSE46872: Collapsing expression values to their median... Using identifier as id variables Now preprocessing raw data of GSE46872: Annotating expression values with SYMBOL... Size of expression...Now preprocessing raw data of GSE21222: Collapsing expression values to their median... Using identifier as id variables Now preprocessing raw data of GSE21222: Annotating e…

Annotation Preprocessing Annotation Preprocessing

updated 12.0 years ago • Manvendra.Singh@mdc-berlin.de

then an error comes as "?????????DGEList(counts = d, group = group) : Length of 'group' must equal number of columns in 'data' " However, length(group) shows that the length of the group is 7, and dim(d) = 37435 7. So I think they two are...equal, so why I got this error? Many thanks! -- output of sessionInfo(): R version 2.9.1 (2009-06-26) x86_64-redhat-linux-gnu locale: LC_CTYPE=zh_C…

edgeR edgeR

updated 13.7 years ago • Guest User

Dear community, I have identified some missing probes on the EPIC array for my analysis using Minfi. Apparently there is no easy way to update this...Mset) <- all_probes Error in `sampleNames<-`(`*tmp*`, value = c("cg18478105", "cg09835024", : number of new names (866616) should equal number of rows in AnnotatedDataFrame (866150)</pre>   Would appreciate if …

Minfi eset

updated 7.9 years ago • SplittingInfinity

<div class="preformatted">Hello, I've been trying to use limma to identify genes from the following data: http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21340 - It's a simple control vs...div class="preformatted">Hello, I've been trying to use limma to identify genes from the following data: http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21340 - It's a simple control

limma limma

updated 13.7 years ago • David Westergaard

m attempting to annotate SNPs from VCF files I have downloaded from the TCGA dataportal. I'm able to identify their locations, but when i try to use the predictCoding() "coding <- predictCoding(vcf,txdb,seqSource = Hsapiens)" to...identify effect of the variants in the coding regions I get the following error  Error in .getOneSeqFromBSgenomeMultipleSequences...sequence ^1$ not fo…

snp variantannotation predict coding

updated 10.5 years ago • vakul.mohanty

a plan to update the guidelines at http://www.bioconductor.org/developers/useDevel/ since the devel version of Bioconductor now requires a new version of R. Thanks! Best regards, Julie [[alternative HTML version deleted]] </div

updated 12.0 years ago • Julie Zhu

previous people, however this specific error was briefly mentioned in a post 3 years ago without identifying the cause of the issue with all solutions commented not working in my case(link to the thread https://support.bioconductor.org...what ends up happening here is that the calculation sf/exp(mean(log(sf))) is saying that every number is NA. However within debugger (giving me temp access to sf…

DESeq2

updated 4.4 years ago • alawrence2211

div class="preformatted">Hi, I want to known that is the build genome version used in affymetrix CDF packages (e.g. : hgu133plu2cdf). I guess in bioconductor 2.7, the gemome build version is the last...one : hg19 GRCh37. I want to use the hg18 version. I think that I must used an old package version like bioconductor 2.6 Thanks Elodie -- Elodie Chapeaublanc IE Bioinformatique

updated 14.8 years ago • Elodie Chapeaublanc

package deals with probes that are mapped to multiple genes. Sure, when I have a single column of identifiers everything works nicely, but what exactly happens when I have more than one gene per probe? I tried a mock annotation...affy=FALSE, prefix="test", fileName=refseqs, baseMapType="refseq", + outputDir=".", version="0.9", manufacturer="GNF-Affymetrix", chipName="gnf1m") Af…

Annotation Annotation

updated 17.4 years ago • Cei Abreu-Goodger

I'm using diffbind to identify differential binding of CUT&tag peaks of H3K27ac. I obtained scaling factors from ChIPSeqSpikeIn package...I'm using diffbind to identify differential binding of CUT&tag peaks of H3K27ac. I obtained scaling factors from ChIPSeqSpikeIn package. I...which you can specify a numeric normalization factor. Could anyone suggest the code to specify number fo…

DiffBind CUT&Tag

updated 23 months ago • Hai

I'm getting an install error I haven't been able to surmount. I'm running R Version 3.3.1 through RStudio Version 0.99.903 on Mac OS 10.10.5. -------------------------------------------- Here is the code I'm running with the error: >rm(list = ls()) &gt...Bioconductor-mirror-BiocInstaller-9965cc7' \\ --library='/Library/Frameworks/R.framework/Versions/3.3/Resources/library' --i…

bioconductor error biocinstaller package installation install

updated 9.1 years ago • matt.s.leslie

I feel like I'm going in circles here. I have R 3.6.0 installed, and it clearly shows this is the version I'm using when I enter the interpreter: $ R R version 3.6.0 (2019-04-26) -- "Planting of a Tree" Copyright (C) 2019 The R Foundation...But then when I try install a package from Bioconductor, it says I'm on an old version and sends me to the exact same website I used to…

software error bioconductor

updated 6.5 years ago • colin.kern

I got this error message when trying to run BiocManager::install() Error: Bioconductor version '3.8' requires R version '3.5'; see https://bioconductor.org/install I have R 3.6, so I have no idea why this error appears

software error

updated 6.6 years ago • romanowska.j

and when I type source("http://bioconductor.org/biocLite.r") I get an error like this: Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade

plasFIA

updated 3.7 years ago • batuhan.caglar1

So far as I can tell, the x and y coordinates of a probe on the array grid are the only truly unique identifiers for a probe on any microarray, and I would like to use these to cross-reference with other data, such as the probe...positions on newer genome versions or even different genomes from related species. The function AnalyzeTilingCel Files appears to output the probe...intensity values - …

probe PROcess genomes probe PROcess genomes

updated 15.9 years ago • Ann Loraine

div class="preformatted">I'd like to figure out the difference between validated miRNAs whose identifiers only differ by a "*". I downloaded the miRNA datasets "hsSeqs" and "hsTargets" and noticed that none of the miRNA identifiers...in dataset "hsSeqs" contains the character "*" whereas many miRNA identifiers in dataset "hsTargets" end with the character "*". I checked a couple of them a…

miRNA miRNA

updated 16.1 years ago • mauede@alice.it

Not all the pathways are returned via list.pathways. I'm trying to get the text definition of identified pathways for example: get.pathways.by.genes('ath:AT5G14780') [1] "path:ath00630" "path:ath01100" yet 00630 is not within...soapArgs = list(org = org), : data length [125] is not a sub-multiple or multiple of the number of rows [63] thanks for the help, and let me know if you need more i…

Pathways KEGGSOAP Pathways KEGGSOAP

updated 14.0 years ago • Guest User

DESeq2 I installed from latest Bionconductor version is still 1.20 version. Actually, the latest version of DESeq2 is >1.4 Pls see below: > source("<a href="https://bioconductor.org...biocLite.R" target="_blank">https://bioconductor.org/biocLite.R</a>") Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for   help > biocLite()  BioC…

deseq2 R bioconductor

updated 7.4 years ago • lxl623

the results(380000 spots) of an analysis into a test file outside R? In the arrays I am using, the number of replicate spots for each probe is not constant. So what value do I use for ndups in fit <- lmFit(MA,design,ndups=?,correlation...0.579) Is there a method in Limma which takes care of such discrepancies in the number of replicate spots for each probe? If not, is there an assumption …

probe limma probe limma

updated 20.6 years ago • Ankit Pal

home they mentioned that Install R 2.15.1. Bioconductor 2.11 has been designed expressly for this version of R. but right now available R version 2.15.2. which one shall i use and older version where i will get?thank u -- output

updated 12.8 years ago • Guest User

yes, exactly this is the problem. But this bug has been fixed in siggenes 1.2.17, the Release 1.6 version of Bioconductor. Best, Holger > --- Urspr?ngliche Nachricht --- > Von: "Sabrina Carpentier" <sabrina.carpentier at="" curie.fr...stat.math.ethz.ch=""> > Betreff: Re: [BioC] [SAM] Error in mat.sig[, "d.value"] : incorrect number > of dimensions > Dat…

updated 20.3 years ago • Holger Schwender

while another group only have 1 cancer microarray. I wonder whether limma could be used to identify differential-expressed genes by comparing these two groups? I am concerned about the accuracy of limma since the

Microarray limma Microarray limma

updated 13.5 years ago • Guest User

here. When I checked the log fold changes I couldn't come to a conclusion. When I counted the number of genes <0, the number is more than 97. Am I doing some thing wrong? 2. If I want to do some pathway analysis, I am wondering...which value I have to use. When I use log fold change values, some genes are not identified as differentially expressed though I gave different cut off values. …

edgeR edgeR

updated 14.5 years ago • puvan001@umn.edu

vignettes), it appears that custom chip packages can only be built by mapping probeset identifiers with gene accession numbers. Since we are not looking at conventional genes, we cannot map our chip probesets...with these gene accession numbers. Is there a another way to link our probeset (using chromosomal location) to public annotations ? Thanks

annotation package custom microarray

updated 10.9 years ago • becker.jeremie

you can see is that it is not a valid installed package. I think I would need to install an older version of R to accommodate for this, does anyone know what version this is? cheers nick > expData <- ReadAffy() > expData AffyBatch...object size of arrays=712x712 features (19 kb) cdf=gnGNF1Ba (??? affyids) number of samples=8 Error in function (package, help, pos = 2, lib.…

Epigenetics cdf Epigenetics cdf

updated 14.0 years ago • Nicholas Wong

I’am running topGO, to perform GO analysis in a RNA-seq data set. I have an small data set of 104 significant genes that I called “sigG”. Firstly, I used genefilter to find genes that have similar level of expression than my “sigG”.  For each sigGene I got 10 genes which make a background set of 1040 genes (backG). I run topGO but I found results that make suspect that something is goi…

topGO gene ontolology rnaseq

updated 8.8 years ago • colaneri

Mon, 2005-02-28 at 04:57 -0800, Robert Gentleman wrote: > Hi, > Bioconductor has a release version (just as R does) and that remains > relatively static through its life, which is typically 6 months. Really > only significant...bug fixes are done on the release version and all new > development is done on packages in the devel version. One main > diffe…

Cancer limma Cancer limma

updated 20.8 years ago • Adaikalavan Ramasamy

suggest any packages in R that can be used to overlay gene expression data on SNP (affymetrix) copy number ? Thanks, Ekta Senior Research Associate Bioinformatics Department Jubilant Biosys Pvt Ltd, #96, Industrial Suburb...any damage caused by any virus transmitted by this email. www.jubl.com [[alternative HTML version deleted]] </div

SNP SNP

updated 13.6 years ago • Ekta Jain

Hi, I'm working with DESeq2 package and i'm stuck in the following situation, My data is from 3 sample (which i call case) grown in 2 different media ```r DataFrame with 6 rows and 2 columns case condition <integer> <factor> 5114_hc 5114 hc 5265_hc 5265 hc 5304_hc 5304 hc 5114_wIR 5114 wIR 526…

DESeq2

updated 3.6 years ago • Davide

typically expected to list the chromosomes or "top-level sequences" so it will always have a small number of entries (i.e. < 100). Things like contigs or scaffolds, which are generally counted by hundreds or thousands, should...go in the 'mseqnames' field. Here they are grouped and stored in 1 (or a small number) of DNAStringSet objects (i.e. < 100) but each object can contain milli…

GO Cancer BSgenome BSgenome genomes GO Cancer BSgenome BSgenome genomes

updated 12.7 years ago • Hervé Pagès

div class="preformatted">Would someone please tell me if there is a way to get the number of samples, GSMs associated with a GSE, from doing a GEOquery that returns GSEs? Specifically, I have this query: sql &lt...So I am getting all the fields I can (I think) for the GSE entries, but I don't see how to get the number of samples for each GSE. I see from the GEOquery documentation that I…

GEOquery GEOquery

updated 16.0 years ago • Dick Beyer

WT using LRT. My problem is that when I remove genes with 0 expression, the results have much lower number of DEGs. Also, after updating some packages (as ashr and mixsqp), I am getting lower number of DEGs when running exactly

DESeq2 filter

updated 2.9 years ago • ayabalbaa1990

Dear All, I would like to ask about using the voom-limma workflow on RNAseq data. Usually, when I run the workflow, the samples contain similar number of reads (translating into a similar number of counts between the samples); however, I have received data for 60 samples, each having 4-5.5M reads, with 2 samples having approximately 26M reads each. My question is whether the voom-limma work…

voom limma RNASeq

updated 4.7 years ago • annadv

div class="preformatted">I have a pile of copy number array results that have been segmented and assigned regional p-values by GISTIC. (I have piles of other data that have...1173.full.pdf="" 31="" 9="" cancerres.aacrjournals.org="" content=""> [[alternative HTML version deleted]] </http:></div

updated 13.5 years ago • Tim Triche

Hi, I would like to get number of beads used to summarize intensity in infinium methylation 450k data and remove intensities based on less than...as follows, nbeads <- assayData(RGset)$NBeads How can do that in lumi? Further, I noticed that number of features are different in MethyLumiM and RGChannelSetExtended classes for same data. Why is it so? > a RGChannelSetExtended

lumi minfi

updated 9.4 years ago • krishna312

genome (around 80 genes) and so the DE analysis. I was wondering if there is a minimum number of genes to be considered to have a correct DESeq2 analysis. And if there are specific parameters to change to do this

DEseq2

updated 7.2 years ago • stefanie.graindorge

is the original file:   \#\#fileformat=VCFv4.1 \#\#source=VarScan2 \#\#INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> \#\#INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates...SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> \#\#INFO=<ID=GPV,Numb…

variantannotation somaticsignatures

updated 9.4 years ago • maria.vila

preformatted">* From the authors webpage (http://bioinf.wehi.edu.au/limma/), the limma package version is 1.8.22 dated 24 February 2005. * From the BioConductor (Release 1.5) webpage http://www.bioconductor.org/repository...release1.5/package/html/limma.h tml the limma package version is 1.8.6 dated 27 October 2004. Is the above discrepancy of nearly 4 months or 15 minor releases intentional…

limma limma

updated 20.8 years ago • Adaikalavan Ramasamy

I need version 3.2.2 of Go.db to answer a question in the Edx PH525.6 course.  Is there anywhere I can download this version from

R go

updated 9.0 years ago • dougoliver48

A only, B only, A+B), I have three biological replicates, for a total of 12 samples. I would like to identify genes that are synergistically affected in the combination condition in addition to the genes that are uniquely

deseq2

updated 6.3 years ago • mattobu83

of time-course (~10 time points) stranded paired-end RNA-seq data with the particular objective of identifying time-dependent changes in alternative splicing. However, I am still undecided whether _alpine_ or _Salmon_...normalisation, I have read the recommendation of "downsampling" reads in order to get comparable numbers for all samples, assuming that the number of reads is roughly equal …

rna-seq salmon alpine transcript expression

updated 7.4 years ago • relathman

div class="preformatted">Hi, How can I cluster GOTerms and assoiciated number of genes from my prob set ids? something like: e.g. GOTERM Number of Genes associated ---------------------------------------------------------------- steroid hormone receptor activity

GO GO

updated 21.2 years ago • Saurin D. Jani

Hi Dears, I may take your few minutes? After DESeq2 analysis, I found pretty small number of significant genes with a cut of point padj < 0.05. When I try with padj < 0.1, it become two much. I wonder if I can use

deseq2

updated 5.5 years ago • Do it!

QC procedures available within GenomeStudio). What I would like to do is to test for recurrent copy number abnormalities across the three platforms, in a way that minimises platform-dependent bias as much as possible. I posted...directed to this paper: A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods http://bio…

SNP Cancer crlmm ffpe SNP Cancer crlmm ffpe

updated 13.6 years ago • Ed Schwalbe

I am seeing a significant different between my own non-integer purity/ploidy-adjusted copy number of segments and the value that PureCN reports in the LOH segments "C" column (usually integer) and I'm trying to understand...averaged over all segments of all samples, is about 0.51 copies. Since C is integer and my copy-number-adjusted values are not, I would expect the mean difference to be about…

PureC PureCN

updated 4.1 years ago • twtoal

Genomic Data Commons hosts [a gene-wise copy number summary][1] for each cancer, which has genes as rows and samples as columns. The column headings are aliquot UUIDs. How...Genomic Data Commons hosts [a gene-wise copy number summary][1] for each cancer, which has genes as rows and samples as columns. The column headings are aliquot UUIDs. How may...matched to other data types, such as a MAF file…

TCGAutils TCGAbiolinks GenomicDataCommons

updated 6.4 years ago • Dario Strbenac

class="preformatted">is there any way (a command o environment variable) to have the bioconductor version? as for R is R.Version() R.version R.version.string ??? -------------------------------------------------- D.Enrique ESCOBAR ESPINOZA (DESS Bioinfomatique B.Sc. Biologie

updated 19.7 years ago • D.Enrique ESCOBAR ESPINOZA

Wondering how everyone is currently using Rsamtools in the newest version of R.  Getting the following: <pre> > install.packages("Rsamtools") Warning in install.packages : package ‘Rsamtools...is not available (for R version 3.4.1)</pre

rsamtools package installation samtools

updated 8.0 years ago • rbronste

1000 probes having larger variances of methylation level across samples. The 1000 probe are identified as chromosome coordinate like following. > rnames[1:10] [1] "chr1:1707145" "chr1:2148663" "chr1:3133683" "chr1:3180808

Microarray Genetics probe charm Microarray Genetics probe charm

updated 13.4 years ago • Yoo, Seungyeul

visible changes. But under the hood this is a thing. it brings in (build) support for newer Java versions and the concept of secondary identifiers. These can be deprecated or alternative identifiers, which are, for example

bridgedbr News

updated 5.1 years ago • egon.willighagen

I have generated a set of primers with openPrimeR, but I got only one set. How can I increase the number of sets returned byopenPrimeR, let's say to 10? Thanks ``` library("openPrimeR") fasta.file <- system.file("extdata", "IMGT_data...fw", settings = design.settings) > sessionInfo( ) R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-…

openPrimeR

updated 4.7 years ago • marongiu.luigi

a problem with biomart driven ensembl querys and it seems that the behaviour depends on the ensembl version used. I'm trying to obtain ggallus homologs for mouse genes on all autosomes and the X. With the May 2015 ensembl archive...I need to query each chromosome in a loop to prevent missing genes, with the March 2015 version I can query all chromosomes at once.   <pre> library(…

biomart ensembl

updated 10.5 years ago • jmeisig

the distribution of expression in different bins and plot them. However, it won't capture gene identifiers of genes (row names) in different bins. I wonder if there is any function in one of the Bioconductor packages / any...90","90-100",">100"))) Thanks in advance for your help. Alan sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86\_64-suse-linux-g…

rnaseqdata clustering

updated 10.9 years ago • Alan Smith

data as a potential discriminator. Ive also used DESeq on the same count data set, which identifies 1569 genes (719 up / 850 down) at padj<0.05. Of these 1569, 1544 are also called by edgeR, so, excellent agreement. Relaxing...a link to the plots: http://inlinethumb04.webshots.com/51523/2373514640050256648S600x600Q85 .jpg R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows" edgeR v…

Sequencing edgeR DESeq Sequencing edgeR DESeq

updated 13.4 years ago • Michael Salbaum

makeCluster" #2 Instantiate CNSet container.Initializing container for genotyping and copy number estimationProcessing sample stratum 1 of 1Quantile normalizing 12 arrays, one at a time. |===================================================================== =====| 100%Calibrating 12 arrays...looks like one of your samples is not like the others (i.e. sample > 6431_8116121004 is not Omni5…

SNP Annotation Normalization crlmm copynumber SNP Annotation Normalization crlmm

updated 11.5 years ago • Abhishek Pratap

of paired samples under two conditions. After performing differential expression analysis, I have identified a substantial number of differentially expressed genes (DEGs) that I would like to prioritize using Weighted

DEGselection RNASeqData WGCNA

updated 14 months ago • Nasim

What should I do to deal with the following sentence? Upgrade 4 packages to Bioconductor version '3.15'? [y/n]: ```r > if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") trying URL 'https://cran.rstudio.com...are in C:\Users\L\AppData\Local\Temp\RtmpA7OiKC\downloaded_packages > BiocManager::install(version = "3.15") 'getOption("repos")' r…

Install

updated 3.2 years ago • dsrlij

Control, Treatment1, Treatment2 & Treatment3) each with duplicate samples. I would like to identify all genes that are significantly differentially expressed across all the 4 groups. Does DESeq2 allow such assessment

deseq2

updated 7.8 years ago • gupta.anuj0608