Bioconductor Forum

probeIDs from 133plus2 arrays to entrezIDs using aafLocusLink, some months ago with an earlier version of the package, and now with the current annaffy and hgu133plus2 packages. I compared my results and some probes no...longer got mapped with the new package version, e.g POU5F1. The gene does have probes on the array, all just happen to be x_at probes. So I thought maybe all those less...probeID…

GO hgu133plus2 probe annaffy convert GO hgu133plus2 probe annaffy convert

updated 16.1 years ago • Merja Heinaniemi

I have one gene that have very high in log2foldchange. <table border="0" cellpadding="0" cellspacing="0" style="width:336pt"> <tbody> <tr> <td> <p>gene</p> </td> <td> <p>baseMean</p> </td> <td> <p>log2FoldChange</p> </td> <td> <p>lfcSE</p> </td> <td> <p>stat</p> <…

deseq2

updated 7.8 years ago • naktang1

confusing messages from the imageplot() function in limma. As in my previous mail, I am using a version of Bioconductor 1.2 from the website from about 2 weeks ago. I am reading the data in from a GenePix file but I want to...And got the error: Error in imageplot(MA, layout = list(ngrid.r = 8, ngrid.c = 4, nspot.r = 16, : Number of image spots does not agree with layout dimensions No…

limma limma

updated 22.4 years ago • michael watson IAH-C

abstract The paper also compares the performance of tweeDEseq against edgeR and DESeq under a large number of scenarios. The results obtained from simulations and real data analysis show that tweeDEseq accurately detects...expected under negative binomial assumption) or heavy tail (e.g, outliers - individuals with large number of counts) among others. Best regards, Juan R Gonzalez, PhD Bioinfor…

edgeR tweeDEseq edgeR tweeDEseq

updated 12.3 years ago • Gonzalez Ruiz, Juan Ramon

e.g. density/ecdf, RNAdeg incorporated in the output? Cheers and thanks, a > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252...Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2…

cdf arrayQualityMetrics cdf arrayQualityMetrics

updated 18.0 years ago • Al Ivens

div class="preformatted">Dear BioC mailing-list, I came across this error using the latest R version and BioMart: > library("biomaRt") > mart = useMart("ensembl") > ensembl = useDataset("hsapiens_gene_ensembl", mart=mart...values = id, mart = mart, : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equa…

GO BSgenome biomaRt BSgenome GO BSgenome biomaRt BSgenome

updated 15.3 years ago • René Dreos

least none that google and I could find). I get the same error whether I use R 2.3.1 or the devel version. I enclose the devel version error. The cels files are read in by ReadAffy and are processed ok by gcrma, however fall...df AffyBatch object size of arrays=1164x1164 features (63518 kb) cdf=HG-U133_Plus_2 (54675 affyids) number of samples=6 number of genes=54675 annotation=hgu133plus2 &a…

Cancer cdf Biobase affy gcrma affyio Cancer cdf Biobase affy gcrma affyio

updated 19.4 years ago • Aedin Culhane

1: In fitCellGrowth(x, z) : Maximal growth reached close to the border. You can identify the well by testing for pointOfMaxGrowthRate. 2: In fitCellGrowth(x, z) : Maximal population reached close to the border...You can identify the well by testing for pointOfMax

cellGrowth warning message

updated 7.7 years ago • muitalegal888

there are 174908 rows. Meaning that 24.03 percent was filtered. 2017-05-08 17:28:10 findRegions: identifying potential segments 2017-05-08 17:28:10 findRegions: segmenting information 2017-05-08 17:28:10 findRegions: identifying...now there are 174908 rows. Meaning that 24.03 percent was filtered. 2017-05-08 17:29:23 findRegions: identifying potential segments 2017-05-08 17:29:23…

derfinder

updated 8.6 years ago • Wayne

microarray, condensing the matrix as a result, doing Pearson correlation coefficient (PCC)  to identify correlation relationships between my genes and other genes that passed filtering criteria using the ‘genefilter...package’. each of my gene use as a query to identify the top 200 genes which shared the most similar expression profile based on PCC. This process is repeated, thi…

R affy mas5 normalization microarray

updated 10.5 years ago • Angel

<div class="preformatted">Hi Josep, > Dear Heidi, > > I am using your package HTqPCR, in order to analyze miRNA taqman plates, > for > which this package is extremely useful. > > For normalization, I used "rank invariant" which selects two miRNAs as the > most "rank invariant". However, as a "sanity check", I wanted to check if &g…

miRNA Normalization GO HTqPCR miRNA Normalization GO HTqPCR

updated 14.5 years ago • Heidi Dvinge

chr3R))), TRUE, propBP) chr3R.random <- DNAString(c2s(chr3R.random)) To extract the number of occurrences of the PWM in the two DNA strings as a function of the minimum score threshold I used this for-loop: outMat...i,3] <- countPWM(pwm, chr3R.random, min.score=c2s(c(outMat[i,1], "%"))) } As expected the number of matches decrease as the minimum score are increased, but much…

Transcription BSgenome Biostrings BSgenome Transcription BSgenome Biostrings BSgenome

updated 16.6 years ago • Kristoffer Rigbolt

DLLpath, ...) : </span> <pre> unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/robustbase/libs/robustbase.so': `maximal number of DLLs reached... ERROR: lazy loading failed

champ 2.9.10

updated 7.8 years ago • sjammula

in bioconductor. On the http://www.bioconductor.org/data/cdfenvs/cdfenvs.html site, there are a number of CDF files for E.coli that can be downloaded. The problem is that there is no such file for the E.coli antisense chip...ecoliasv2" and "ecoli" chip (please refer to the URL). I was wondering if these chips are different versions to the one I am using, in which case I can probably use them . …

cdf cdf

updated 21.8 years ago • Ilhem Diboun

<div class="preformatted">Hi dear list, My question is on meta-analysis. I have three studies on the association of a SNP with a disease and I need to do a random-effects meta-analysis with my data. I only have the individual P value, the odds ratio and sample size from each study. I've checked rmeta and meta packages but it seems to me that I need to know the number of observations on eac…

SNP SNP

updated 15.5 years ago • Laura Rodriguez Murillo

of this type of analysis if they have any advice for experimental design, in particular, the number of replicates they have used and why (I was planning on going for all biological replicates, no technical). Thanks Mick...alternative HTML version deleted]] </div

edgeR DEGseq DESeq edgeR DEGseq DESeq

updated 15.6 years ago • michael watson IAH-C

Hi, <span style="line-height:1.6">I'm using DEXSeq and would like to do some filtering base on the minimum count number for each exon. With the default parameter, DEXSeq reports many significant events, many of which seem to have lower counts...line-height:1.6">I'm using DEXSeq and would like to do some filtering base on the minimum count number for each exon. With the default parameter…

dexseq

updated 11.1 years ago • liaojinyue

months of graduation. *The Telegraph The University of Stirling is a charity registered in Scotland, number SC 011159. [[alternative HTML version deleted]] </div

gage gage

updated 12.1 years ago • Christian De Santis

columns for the two channels. This generates an error: Error in "[<-"(*tmp*, , i, value = NULL) : number of items to replace is not a multiple of replacement length. Thank you, Juerg Straubhaar [[alternative HTML version deleted

Microarray Microarray

updated 22.4 years ago • Straubhaar, Juerg

4 gene3 1 0 . . . how to do this in R, i tried merge but i found significant increase in number of rows. Any help is appreciated Best Regards, Chris [[alternative HTML version deleted]] </div

Cancer Cancer

updated 12.5 years ago • chris Jhon

function, but it is very slow for large DNAStringSets. Is there a way to quickly calculate the number of differences between two DNAString instances? For example, let's say I have two DNAStrings: "ACAC" and "ACAG". I would like...the distance between them is 1. Thanks in advance for any help. - Erik [[alternative HTML version deleted]] </div

updated 15.8 years ago • erikwright@comcast.net

could help me figure out the same. The package works fine for the gene data with whole number or integer values. How can I run the analysis for decimal data as the class newCountDataset does not allow me to input...be great if you could help me through this. Thanks Regards Suryavadhan [[alternative HTML version deleted]] </div

DESeq DESeq

updated 14.3 years ago • Kayilai, Suryavadhan MU-Student

<div class="preformatted">Hi everyone, I'm using the LiWongRank function in RNAither to do with my data. Here's the code of the example that is failing: > data(exampleHeader, package="RNAither") > data(exampleDataset, package="RNAither") > normres <- LiWongRank(header, dataset, list("SigIntensity", "GeneName")) Then the function needs user input the threshold to …

RNAither RNAither

updated 14.5 years ago • Ning

<div class="preformatted">Hi, I just wonder what kind of system ( cpu type, speed and amount of physical memory ) do you use for data analysis. Because I think most of Wintel users are suffered from memory handling problem and computing time. Ben Bolstad kindly offered computing time by cpu speed, memory, array type and number of arrays in his AffyExtensions vignettes. This kind of informa…

Microarray Microarray

updated 22.3 years ago • Sek Won Kong, M.D

exprs'. But I couldn't figure out how to do this for essGene(). In the latter case I get "incorrect number of dimensions". So I need to tweak the input, question remains, how... Thanks Chris [[alternative HTML version deleted]] </div

updated 12.9 years ago • Forst, Christian

description here][1] I got a 16 up-regulated gene from DESeq2 result. However, when I count number of upregulated gene using excel with same threshold (paj<0.05, logfoldchange >1) I got a 211 up-regulated gene. ![enter

RNASeqData DEGseq

updated 2.4 years ago • sybyun419

<div class="preformatted"> Hi, I am beginner with Lumi and I manually copy/paste the median and quantile values from each sample in the MAplot(lumi.N) pdf to identify the >xSD outliers. Could you please help me with R commands that I can use to save these values for all sample on a table...I manually copy/paste the median and quantile values from each sample in the MAplot(lumi.N) pd…

lumi lumi

updated 14.1 years ago • Guest User

preformatted"> hello I get data(GSE37527) from GEO database and I am trying to analyze(normalize and identify DE) them in to R with package AgiMicroRna. Does my Data fit with this package. In my data doesn't exist the columns gMeanSignal...package is better than another. Please help me thanks in advance -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x6…

GO GO

updated 12.9 years ago • Guest User

1. Get an expression table for both datasets (U219 and U133) 2. label both datasets with "comparable" identifiers, eg UniGene Id or GeneBank A# 3. get new expression tables with only entries present in both datasets Second scenario...that there are only perfect match probes on the HG-U219 and no MMs? [[alternative HTML version deleted]] </div

Normalization convert ArrayExpress Normalization convert ArrayExpress

updated 14.8 years ago • Andreas Heider

I am writing here because I would like to replicate the maSigPro methodology (maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments, Ana Conesa et al. (2006...Many thank for your precious help. Best regards, Paola Tellaroli -- output of sessionInfo(): R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) local…

maSigPro maSigPro

updated 12.2 years ago • Guest User

is considered less stringent than the > others. Does this mean least "stringent" in terms of > identifying DE genes? > So is this method also considered to be the most > conservative- eg it identifies > fewer gene and...at say the 0.05 level so > I realize then that within > my list of DE genes, the expected number of FPs is > less than 5%. …

probe limma probe limma

updated 19.2 years ago • noel0925@sbcglobal.net

Bioconductor called 'qpgraph'. This package *does not* address what you are asking for, namely to identify interaction terms in a transcriptional regulatory network from microarray data, since the package assumes that...break down in the presence of interacting terms. however, i think it could help you to reduce the number of candidate subsets of TFs where you would try the approach you're propo…

Transcription Microarray Network qpgraph Transcription Microarray Network qpgraph

updated 16.9 years ago • Robert Castelo

to look at differential gene expression. For some of the comparisons of interest, a strikingly low number of differentially expressed genes was reported. Cuffdiff reported many  more genes as differentially expressed...account for the large difference in DEG calls between Cuffdiff and DESeq2? > sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86\_64-apple-darwin13.4.0 (6…

DESeq2 RNASeq differential gene expression

updated 8.5 years ago • A

Hello After having noticed some spurious results in my data set I wanted to contact this expert community here to get help with choosing the right normalization approach for my data. I have two groups, patients and healthy controls, where microbiota OTUs have been measured from biopsies: Quality filtering was performed using SDM software and default criteria parameter adapted to the 454 sequenc…

deseq2 normalization R edger

updated 7.8 years ago • apfelbapfel

The demographic profile includes a diverse mix of age groups, ethnicities, and socio-economic backgrounds. Key health issues identified through data collection methods such as surveys, health records, and community meetings include high rates of...includes a diverse mix of age groups, ethnicities, and socio-economic backgrounds. Key health issues identified through data collection methods such as…

genomes

updated 15 months ago • Arthurella

a bit unclear on the best way to proceed- any insights would be greatly appreciated. I want to identify a set of genes that are co-regulated with a given phenotype that is observed across various tissue types -to ID the...between 1A (relative only to 2A and 3A) and 1B (relative to 2B, 3B, and 4B). I have varying numbers of replicates per condition (2-5). I have done unsupervised clustering usi…

GO Clustering GO Clustering

updated 21.6 years ago • Luckey, John

able to re-analyze old data. Particularly, I have data from the Mouse WG 6 v1_1 read by BeadStudio version 3.0.14 I would like to still be able to use this data, but with the new annotation packages with NuIDs. I currently get...me wonder if all the old target IDs are actually in the "lumiMouseIDMapping" file: More than 500 identifiers cannot be found in the library:lumiMouseIDMapping.db! T…

updated 17.2 years ago • Cei Abreu-Goodger

org.Hs.eg.db) x <- org.Hs.egSYMBOL # Get the gene symbol that are mapped to an entrez gene identifiers mapped_genes <- mappedkeys(x) # Convert to a list xx <- as.list(x[mapped_genes]) eids <- '' ENTREZID2GENESYMBOL &lt...wrong in my code (or libraries/functions used)... many thanks! Tim PS: My sessionInfo() is : R version 2.8.0 (2008-10-2…

Cancer Homo sapiens convert Cancer Homo sapiens convert

updated 16.8 years ago • Tim Smith

genes with the default p.value argument (p.value = 1): ```r topTable(fit, coef = 2, confint = 0.95, number = 3) # p.value = 1 (default) ``` ``` logFC CI.L CI.R AveExpr t P.Value adj.P.Val B Gene 2 2.104 1.616 2.59 1.070 10.15 1.67e-05 0.00167...output after supplying a p.value = 0.5: ```r topTable(fit, coef = 2, confint = 0.95, p.value = 0.5, number = 3) ``` …

limma

updated 4 months ago • sandmann.t

Hi, I Have installed the most recent Champ version 2.9.10 ChAMP.load gives me the error message: Error in champ.load(directory = getwd(), method = "ChAMP", methValue = "B",&nbsp...DLLpath = DLLpath, ...):  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/mvtnorm/libs/mvtnorm.so':   \`maximal number of DLLs reached... In…

ChAMP champ 2.9.10 methylationepic

updated 7.8 years ago • david.ch

AffyBatch object size of arrays=230x230 features (11 kb) cdf=miRNA-1_0_2Xgain (??? affyids) number of samples=9 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment...www.bioconductor.org=""> mirna10probe. R und Bioconductor are installed last week, but also in older versions it doesnt work. Thank you very much Claudia Döring …

miRNA Microarray cdf miRNA Microarray cdf

updated 15.1 years ago • Claudia Döring

following error: <pre> > source("http://bioconductor.org/workflows.R") <strong>Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help</strong> <strong>Error: BiocInstaller:::BIOC_VERSION == "3.1" is not TRUE</strong...I see this  <pre> source("http://bioconductor.org/biocLite.R") # FIXME, don't hardcode version number stopifnot…

workflows installation biocinstaller

updated 9.9 years ago • davide risso

Hello everyone, I'm trying to get some sequences surrounding SNPs, but I get the error message below. Any solutions? Error message: ```r Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = 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. …

biomaRt bioma

updated 2.7 years ago • Luca

I used vsn to normalize and limma to find differentially expressed genes. I used "topTable" with number=Inf and p.value=0.05 to get all significant genes for a given condition, regardless of their fold change. I seem to be...mat = model.matrix(~f, ALL) lm = lmFit(ALL, mat) eb = eBayes(lm) sign = topTable(eb, coef=2,number=Inf,p.value=0.05) dim(sign) sort(2^sign$logFC) > sessionInfo() R …

Microarray vsn limma Microarray vsn limma

updated 15.1 years ago • Eva Benito Garagorri

<div class="preformatted">Dear all, I perform 2 color hybridization, using microRNA and Exiqon slides. slide design: 4 replicates of 1 array each array consits of 8 subarrays, each subarray of 16 columns and 11 rows each mir has 4 replicates For analysis of the data I use limma GUI, to obtain the p-values of differentially expressed…

GUI limma microRNA GUI limma microRNA

updated 17.2 years ago • Christine Voellenkle

lpe.val, adjp="BH") > fdr.2 <- fdr.adjust(lpe.val, adjp="resamp", iterations=2) iteration number 1 is in progress iteration number 1 finished iteration number 2 is in progress iteration number 2 finished Computing...I dont get any adjusted p values any suggestion ? thanks Philippe ps I ve been also trying the old version of LPE without permutation lpe.val1<-data.frame(lpe(da…

LPE LPE

updated 21.9 years ago • Phguardiol@aol.com

object)'Annotation: moex10stv1  sessionInfo()      # gives :R version 2.7.0 (2008-04-22) x86_64-unknown-linux-gnu locale:Cattached base packages:[1] splines   tools  &nbsp...www-bio3d- igbmc.u-strasbg.fr/~wraffwolfgang.raffelsberger@igbmc.fr [[alternative HTML version deleted]] </div

Annotation affy Annotation affy

updated 17.5 years ago • Wolfgang RAFFELSBERGER

Tan <daren76 at="" hotmail.com="">: > > Please clarify my understanding. > > When R version 2.8.0 was released, all packages in Bioconductor > version 2.3 was built with it. During this period, any installation...gt; of packages in bioconductor 2.3 did not give any warnings. With the > minor release R version 2.8.1, Bioconductor version 2.3 was reb…

updated 16.8 years ago • Patrick Aboyoun

Hi Rory, I am using DiffBind to identify sites differentially bound (affinity analysis) by a transcription factor in control (WT), heterozygous (HET), and knockout...default normalization method and spike in normalization. The results are similar for both. DiffBind identifies a good number of sites that are significantly differentially bound between WT and KO. Comparing HET v. KO shows...50% re…

DiffBind

updated 3.5 years ago • ipsc-jl

the VCF offline, as it is human data.  In the example, it seems that after expansion, the `` AD `` numbers appear to not match the `` CollapsedVCF `` version.   <pre> > vcfCompressed = readVcf('abc.vcf','hg19') > vcfExpanded = expand...DataFrame with 14 columns: DB, ECNT, HCNT, MAX_ED, MIN_ED, NLOD, PON, RPA,... info(header(vcf)): Number Type…

VariantAnnotation bug

updated 9.1 years ago • Sean Davis

pre> Package: ErrorReproducer Type: Package Title: Error Reproducer Date: 2015-5-11 Version: 0.99.1 Author: Human Maintainer: Human <human@species.org> Depends: R (>= 3.1.0), methods Suggests: BiocGenerics...the test returns no errors. <pre> RUNIT TEST PROTOCOL -- Mon May 11 15:19:01 2015 *********************************************** Number of test fu…

software error cmd check bioconductor

updated 10.6 years ago • Wade Copeland

got the normalized data file with 17000+ probes and 283 samples. I tried to associate the ID\_REF numbers (example "6747308") using the moex10stprobeset.db, the dataset says they used "\[MoEx-1\_0-st\] Affymetrix Mouse Exon 1.0...ST Array \[transcript (gene) version\]". I keep getting an error message that says the probe ids are not valid for that database. Are these numbers not actually

annotation affymetrix

updated 7.7 years ago • trhood

CNV size using affy SNP 6.0 (Integrated detection and population-genetic analysis of SNPs and copy number variation). The sensitivity of Illumina 1M was 47% in another paper (Systematic assessment of copy number variant detection...one should prefer one platform over the other. best regards, // Johan [[alternative HTML version deleted]] </div

SNP Genetics Coverage CGH affy SNP Genetics Coverage CGH affy

updated 17.0 years ago • Johan Lindberg

541825 2 According to this code, I've extracted a total of 541825 exons which are associated with x number of genes. Now when I do the following: length(unlist(annotDf[, 'gene_id'])) [1] 546664 How is it possible that there are suddenly...using allExons and reads from a bam file. This command is failing because it seems that the number of gene_ids is not pairing up with the exon_ids properly…

GenomicFeatures GenomicFeatures

updated 13.0 years ago • Fong Chun Chan

Hi, I have been trying to install EnsDb.Hsapiens.v75 or other versions of it including v.79, and I got some warning and error messages. I think it might be because I am using M2 Mac chip, and

EnsDb.Hsapiens.v86 EnsDb.Hsapiens.v79 EnsDb.Hsapiens.v75

updated 3.3 years ago • Taeim

offers RefSeq mapping if I understand - knowing that you are limited to the genbank accession number attribution for a probe set offered by Affymetrix. Thanks for any help/comments David [[alternative HTML version deleted

GO GO

updated 20.8 years ago • Rickman David

data(quakes) Depth <- equal.count(quakes$depth, number=8, overlap=.1) jpeg("3.jpeg") xyplot(lat ~ long | Depth, data = quakes) dev.off() ###it's ok for(ind in 1:10){ jpeg(paste((1:10)[ind],".jpeg",sep="")) xyplot...any suggestions? --- LiGang [[alternative HTML version deleted]] </div

updated 17.3 years ago • li lilingdu

It would be great to have directly a way where i can impute the statistic, the BP and the chr number and to obtain the plot together with the regions of the chromosome. Any suggestion or idea would be appreciated... thanks..._________________________________________________________________ [[alternative HTML version deleted]] </div

CGH impute CGH impute

updated 16.8 years ago • Giulio Di Giovanni

lmFit(file[,-1], design=group) # Column 1 contains row-names fit2 <- eBayes(fit) topTable(fit2, number=Inf, adjust.method="BH")$t I am not sure how to obtain the values of topTable() along with the corresponding row names. Could...you please advise. Thank you. Cheers, Chintanu [[alternative HTML version deleted]] </div

updated 13.6 years ago • Chintanu

the genes of two different pathways are correlated or anti-correlated or no correlation at all. The number of genes in the two pathways are different, that's why a simple scatter plot will not be effective. Is there a simple way...Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]] </div

Pathways Pathways

updated 13.0 years ago • Alyaa Mahmoud