Bioconductor Forum

RMA in R for my datasets with Affymetrix platform (HGU133plus2). But my problem is i am getting duplicate gene symbols with different expression values. What step can i do to get unique gene symbols. Please help me out

normalization

updated 8.5 years ago • lily

3)) wg <- as.numeric(x) anova(lm(wg ~ gr)) } data <- read.table("file", header=T, sep = "\t", row.names=1) res <- array() res <- apply(data, 1, my.anova) res <- data.frame(res, row.names = row.names(data)) write.table(res, quote

Microarray affy Microarray affy

updated 22.1 years ago • Isaac Neuhaus

mart2)) if (is.null(hum)==FALSE) # if a homolog was found { #A duplicate removal stage if(dim(hum)[1]>1) { j=1 # the first entry in hum to check for duplicates k=dim(hum)[1] while(j<k) if(length(which...hum="hum[j]))" {="">1)# if there is a duplicate …

convert biomaRt convert biomaRt

updated 17.9 years ago • Steve Pederson

<div class="preformatted">Dear Bioconductor list, I am analysing data from a custom Agilent array with 3600 spots using Limma. There are 3 probes for each gene (usually, however some genes only have one probe), all probes are in duplicate. I would like to obtain an average M value for each gene. Examples of the spot ID's are as below. D137-cbdb_A1587_1 D137-cbdb_A1587_1 D137-cbdb_A1587…

updated 15.7 years ago • alison waller

interesting to see that read.ilmn() generates some extra rows. It turns out that the extra rows are duplicates, possibly due to the different decimal points from different data sets when I combined the data from different...chips together. How do I remove the duplicates (keep only the first row) for the ElistRaw class, x ?? I simply merged different data sets to keep only shared probeIDs

limma limma

updated 10.6 years ago • Rao,Xiayu

not full rank':__ __  vignette('DESeq2')__ I read in the DESeq2 manual that DESeq works on duplicates. My questions are: 1) Is there any case where I can use DESeq2 without duplicates? How am I to go about doing it? 2) I tried

deseq2

updated 7.1 years ago • csijst

<div class="preformatted">Hi, I have created eSets from RGLists for cDNA microarrays. I would like to combine in the end data from several different platforms. As a special case, I would like to combine 2 eSets with the same gene probes, but in a different order on the array (so 2 different array platforms). The IDs of my probes are not unique, so I cannot use them as FeatureNames...some h…

updated 17.5 years ago • Vanessa Vermeirssen

<div class="preformatted">Dear Wonjong, > Date: Wed, 18 Apr 2007 17:46:29 -0700 > From: "Wonjong Moon" <wonjong.moon at="" sbri.org=""> > Subject: [BioC] Duplicated spots in limmaGUI > To: <bioconductor at="" stat.math.ethz.ch=""> > > Our slide design had some spots were duplicated and some were not. > I am using limmaGUI, The d…

limmaGUI limmaGUI

updated 17.9 years ago • Gordon Smyth

I have a RNASeq data-set which consists of 4 different conditions (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...consists of 4 different conditions (Control, Treatment1, Treatment2 & Treatment3) each with duplicate samples. I would like to ide…

deseq2

updated 7.1 years ago • gupta.anuj0608

I have duplicate samples for RNAseq and just wonder if there is way to test if the replicates are good or not and what criterion

RNASeq

updated 10.0 years ago • Fix Ace

for the values returned by se.exprs? Is there a way to perform a significance analysis WITHOUT duplicate arrays? For example, if you have two arrays for each of two treatments you can use multtest to identify differentially

multtest multtest

updated 21.9 years ago • Ann Hess

with different start and end positions? Also is there a way to automate deleting these gene duplicates? ![enter image description here][1] . \ [1]: /media/images/851d20fc-9b50-412f-bd42-4e11eab1

biomaRt

updated 3.3 years ago • adeler001

Matrix with a list of Gen-Symbols obtained from the annotation-file, but as some Gen-Symbols are duplicates, this causes some issues.   Thanks in advance

expressionset bioconductor

updated 8.5 years ago • bi_Scholar

I get warning message: ``` Warning messages: 1: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames ``` Could any one please explain to me what this means? The last line...contig=<id=chr6,length=171115067> ##contig=<id=chr7,length=159138663> ``` I do not see duplications.</id=chr7,length=159138663></id=chr6,length=171…

software error

updated 6.0 years ago • Haiying.Kong

vignette in order to improve the result, and I got an error. The point is, I tried very specific duplicate removal for my data set (a.k.a, list of GRanges), for the matter of efficiency, I tried data.table solution and it worked...object with `` name, score, p.value `` is its metadata. This is my data.table solution to apply duplicate removal for my data: <pre> <span style="background…

r compilation error error handling data.table

updated 8.2 years ago • Jurat Shahidin

file, as.integer(yieldSize), maps$samples, maps$fmap, maps$imap, maps$gmap, row.names) setNames(result, "*:*-*") }, scanTabix_io = function(err) { stop("scanVcf: ", conditionMessage(err), call. = FALSE) }, error = function(err...geno = vcfGeno(param), samples = vcfSamples(param)) 12: scanVcf(file, param = param, row.names = row.names, ...) 11: scanVcf(fi…

ensemblvep

updated 7.8 years ago • mlrubio

Hola buen día, soy nueva en esto y tengo problemas para analizar estos datos. Cualquier ayuda estaría muy agradecida. Quiero hacer un análisis de anotación funcional pero siempre obtengo la misma señal de error. Estoy usando el paquete: org.At.tair.db Veo los argumentos validos y he intentado con todos, pero ninguno funciona: columns (org.At.tair.db). La base de datos que estoy utilizan…

DUDAS org.At.tair.db

updated 4.1 years ago • lore

data=exprs2,varMetadata=mData) At this step I have the following error: Error in `row.names<-.data.frame`(`*tmp*`, value = c("A", "B")) : length of 'row.names' incorrect It seems strangle because "A" and "B" are the colnames of...of pData). I tried to do : metData<-new("AnnotatedDataFrame",data=exprs2,varMetadata=mData, row.names=1) or rown=rownames(exprs) metData&…

Survival Yeast Biobase genefilter tkWidgets marray convert arrayMagic affyio Survival

updated 17.6 years ago • Yad Ghavi-Helm

is it possible in the current version? We have 6-7 biological reps for each of 4 treatments, and duplicate technical reps and would like to incorporate this into the analysis. thanks simon.</div

limma limma

updated 21.1 years ago • Simon Melov

Are repeated measures anova with limma(IE using duplicate correlation and a blocking variable and a measurement covariate) directional?  Will it automatically test

limma

updated 10.2 years ago • kodream

gt; annotation package or am I having problems installing it > on my computer? This is a duplicate message (not the sender's fault, our fault). Nianhua has answered already. Summary is that, yes, there is a problem with

Annotation Annotation

updated 18.8 years ago • Seth Falcon

y$counts))] norm_factor_inputs <- calcNormFactors(y_inputs) y$samples$norm.factors[grep(".[i]..",row.names(y$samples))] = norm_factor_inputs y$samples$norm.factors[grep(".[p]..",row.names(y$samples))] = norm_factor_inputs y$samples...norm.factors[grep(".[r]..",row.names(y$samples))] = norm_factor_inputs y$samples So what I'm basically trying to do is calcNormFactors for just the inputs

edgeR edgeR

updated 10.9 years ago • Scott Daniel

containing normalised microarray data: exp = as.matrix(read.table("rma.txt", header=TRUE, sep="\t", row.names=1, as.is=TRUE)) pd = read.table("groups.txt", row.names= 1 , header = TRUE, sep="\t") meta = data.frame(labelDescription = c("Age of...patient"), row.names=c("age")) pheno = new("AnnotatedDataFrame", data=pd, varMetadata = meta) works to here. but then it fails here: my_set = new("Exp…

Microarray Microarray

updated 16.7 years ago • Nathan Harmston

Greetings, I'm getting the following error when calling glmQLFTest() <pre> > qlf <- glmQLFTest(fit,contrast=cont.matrix) Error in data.frame(logFC = logFC, logCPM = glmfit$AveLogCPM, LR = LR, : 'row.names' should specify one of the variables > traceback() 4: stop("'row.names' should specify one of the variables") 3: data.frame(logFC = logFC, logCPM = glmfit…

edger

updated 7.4 years ago • david.powell

hi! I use monocle to make a pseudotime anlysis with my single cell sequencing data. After dimension reduction and cluster, when I try to order cells using the function "orderCells",the error occurred. The error is: "Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:519" The code i use is showe…

scRNA monocle packages Tutorial

updated 5.6 years ago • 444579004

final result were as follows: Error in data.frame(full = c("19851", "19917", "17545"), vs. = c("0", : duplicate row.names: I would be so obliged and grateful to get a solution Thanks Manu ***************************************** Manvendra Singh AG Izsvak - Mobile DNA

Annotation Preprocessing Annotation Preprocessing

updated 11.3 years ago • Manvendra.Singh@mdc-berlin.de

colnames(counts) %in% rownames(cluster_metadata))])" for my 3-cell analysis because I can't have duplicate rownames for cluster_metadata. The row names of the metadata are sample names. But the samples would be the same...for each cell type so there would be 3 duplicates for each sample (one for every cell type). Is there another way to look at multiple subsets of cells at once? Or should

pseudobulk DESeq2

updated 13 months ago • puffsquash

hgCutoff,testDirection = "over") Warning messages: 1: In makeValidParams(.Object) : removing duplicate IDs in geneIds 2: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds > > over_kegg<- hyperGTest

Microarray Annotation GOstats Microarray Annotation GOstats

updated 16.3 years ago • Legaie, Roxane

<div class="preformatted">Dear Sir I am a novice to limma. I meet some questions and can't solve these by myself. So please give me a hand. firstly, I wonder could I use two wt.fun to filter bad spot, for example: myfun1 <- function(x, threshold=50) { + okred <- abs(x[,"F635 Median"]-x[,"F635 Mean"]) < threshold + okgreen <- abs(x[,"F532 Median"]-…

Microarray limma Microarray limma

updated 19.7 years ago • ? ?

the error disappears but my gene names are not conserved in the heatmapSig(). My design matrix has duplicate samples in a column but I beleive the ndups is only for feature names, correct? I hope the following is clear but if

limma ndups htqpcr software error

updated 9.6 years ago • julio.c.silver

six columns are required, and either the column "svclass" > (deletion, translocation, tandem-duplication, or inversion) or the > columns "strand1" & "strand2" (BRASS convention) must also be present [1]: https://github.com

StructuralVariantAnnotation

updated 8 months ago • Dario Strbenac

<div class="preformatted">I am relatively new to R and EdgeR. In the similar package DEseq, there is the possibility of analyzing a dataset containing replicates only for one condition, but not for the other. In this DEseq case only the condition with replicates is considered to compute the dispersion. In the part of the User Guide of EdgeR regarding "working without duplicates" this is not…

edgeR DESeq edgeR DESeq

updated 11.9 years ago • Teresa

reads + QC-failed reads) 23008511 + 0 primary 0 + 0 secondary 0 + 0 supplementary 1391376 + 0 duplicates 1391376 + 0 primary duplicates 23008511 + 0 mapped (100.00% : N/A) 23008511 + 0 primary mapped (100.00% : N/A) 23008511 + 0 paired

subread featureCounts

updated 2.4 years ago • dario.beraldi

<div class="preformatted">I also have a data set with differing numbers of spot replications. I used lme to analyze these data, gene by gene. Basically, I wrote a little function that pulls the spot information out of the array, removes the flagged spots and does other data cleaning, and then runs lme (using "try" in case it bombs). Then I use "split" to split the array data by geneID, a…

limma limma

updated 21.3 years ago • Naomi Altman

Hi, I am using DoubleTrouble to analyze the duplicate genes in my aim genome. I met error when I used the classify_gene_pairs function: ```r > YY.class <- classify_gene_pairs

syntenet doubletrouble

updated 12 months ago • hfyuan2016

SOFT files for co expression analysis.That contain probe list with the expression value of sample, duplicate probes are existing.So kindly  share your valuable ideas and suggestions to SOFT files Thank you Best Regards

WGCNA geo data

updated 8.2 years ago • mathavanbioinfo

library(edgeR) Read\_counts=read.delim("Table.txt",row.names = "Gene") counts=subset(Read\_counts,Read\_counts$Control >= 10 | Read\_counts$Case >=10) y=DGEList(counts=counts,group...fdr, file="fdrcorrection.csv") raw=data.frame(et$table) DEResult\_Counts=merge(counts,raw,by="row.names",row.names=FALSE) write.table(as.data.frame(DEResult\_Counts),"DEResult\_with\_C…

edger

updated 9.2 years ago • Sushant Pawar

package="matchprobes") pd1 <- new("AnnotatedDataFrame", data=data.frame(fromFile = I(f1), row.names="f1")) pd1 pd1 <- new("AnnotatedDataFrame", data=data.frame(fromFile = I(f2), row.names="f2")) pd1 <- new("AnnotatedDataFrame...data=data.frame(fromFile = I(f1), row.names="f1")) pd2 <- new("AnnotatedDataFrame", data=data.frame(fromFile = I(f2), row.names="f2")) x1&l…

cdf cdf

updated 16.3 years ago • Rifat A Hamoudi

attr(,"package") [1] "DEXSeq" > write.table(results, "dexseq.tsv", sep="\t", quote=F, row.names=F) Error in write.table(results, "dexseq.tsv", sep = "\t", quote = F, row.names = F) : unimplemented type 'list' in 'EncodeElement...lt;- as.data.frame(results) > write.table(df_results , "dexseq.tsv", sep="\t", quote=F, row.names=F) Error in write.table(df_results, "dexseq.t…

DEXSeq

updated 10 months ago • Sara

lt;-read.table("~/Desktop/Internship/Extracted CP.Auto genes from RNASeq batch_1.txt",header=TRUE, row.names = 1) countdata <- as.matrix(countdata) (condition <- factor(c(rep("AUTO", 69), rep("CP", 120)))) library("DESeq2") (coldata <- data.frame...row.names=colnames(countdata), condition))</code></pre> <p>After I input the last line, I get this error me…

deseq2 R genomics

updated 7.1 years ago • mokunf

sigmet.idx.hs\] head(kegg.sets.hs, 3) bckCountTable <- read.table("Matrix.txt", header=TRUE, row.names=1) samples <- data.frame(row.names=c("R1", "R2", "R3","IR1","IR2", "IR3"), condition=as.factor(c(rep("R",3),rep("IR",3)))) samples bckCDS <- DESeqDataSetFromMatrix...mapIds(org.Hs.eg.db,             &…

Pathview probe

updated 7.6 years ago • Luiz

data. I counted the probes for each "gene" and added to get a total of 281966. Am I missing duplicates? What am I doing wrong? My objective is to merge the CEL and CDF files so that I can perform my own analysis.</div

hu6800 cdf hu6800 cdf

updated 21.9 years ago • Ann Hess

Is it possible to use RNA-seq tools for getting P-values for gene duplication detection based of gene coverage? I have a list of genes vs read counts. I thought about: 1. mapping reads of wild...Is it possible to use RNA-seq tools for getting P-values for gene duplication detection based of gene coverage? I have a list of genes vs read counts. I thought about: 1. mapping reads of wild type

edgeR

updated 8.8 years ago • biotech

library( edgeR ) > library( dplyr ) > a01 <- read.table( "a01.txt", sep = ",", header = T, row.names = 1 ) > a02 <- read.table( "a02.txt", sep = ",", header = T, row.names = 1 ) > a03 <- read.table( "a03.txt", sep = ",", header = T, row.names = 1 ) > a07...lt;- read.table( "a07.txt", sep = ",", header = T, row.names = 1 ) > a08 …

edgeR

updated 5 months ago • hiroko.ohmiya

<div class="preformatted">Hi I want to compare DESeq vs DESeq2 and I am getting different number of DEGs which I will expect to be normal. But when I compare the 149 genes iD that I get with DESeq with the 869 from DESeq2 there are only ~10 genes that are in common which I don\'92t understand (using FDR <0.05 for both). I want to block the Subject effect for which I am including the…

DESeq DESeq2 DESeq DESeq2

updated 10.8 years ago • Catalina Aguilar Hurtado

<div class="preformatted"> Dear mailing list, I am doing dual color hybridization using the last version of the miRNA microarrays from exiqon ("7th generation"). Applying the limma package, data are background corrected (normexp) and normalized (global loess), subsequently the 4 duplicates of each miRNA species are correlated (DupCor) and lmfit is performed. I used the following script, wh…

limma limma

updated 12.5 years ago • Guest User

answer it. here is my SampleSheet. ![1][1] last.BAM was compared to the genome.Mitochondrial duplication, PCR duplication and low-quality reads were removed. Paired-ended sequencing to the same chromosome ![2][2] figure2

ATACSeq DiffBind

updated 2.7 years ago • young

columns nspot.r <- # rows within each grid nspot.c <- # columns within each grid ndups <- # duplicate spots spacing <- # spots between duplicate spots npins <- # print pins in the print head that printed the array start

Microarray limma Microarray limma

updated 19.4 years ago • David Henderson

spot. This is not really desirable as I would like to see (ideally) a triplicate or at least a duplicate of spots distributed for each gene to allow some kind of quality check (variability) as well as use some of the more...point me to any published papers or working papers on slide design that cover these points: * single/duplicate/triplicate/many spots * advantages of replicate slides and dye …

Microarray affy Microarray affy

updated 21.8 years ago • William Kenworthy

let me tell you how to imported the data etc  countdata<-read.table("data.txt",header=TRUE,row.names=1) conds<-as.factor(c("Treated","Control")) coldata <- data.frame(row.names=colnames(countdata), conds) dds=DESeqDataSetFromMatrix

deseq2

updated 8.9 years ago • Nemo

<div class="preformatted">On spotted arrays with duplicate spots for each gene, I would like to extract all the normalized expression values for each gene. How can I do this? Thanks...div class="preformatted">On spotted arrays with duplicate spots for each gene, I would like to extract all the normalized expression values for each gene. How can I do this

updated 21.5 years ago • Naomi Altman

and 24h, 48h, and 72 hour samples are taken. We now have 12 arrays (4x 3 time points) and its duplicate. I searched for some methods for the analysis of this kind of data, yet I could not find one. Could you please advise

updated 18.1 years ago • Ozge Gursoy-Yuzugulu

lt;- t(as.data.frame(geno(all_vcf_PASS)$ADT[which(geno(all_vcf_PASS)$GT != '.', arr.ind=T)],row.names=NULL)[1,]) > normal_ref_support <- t(as.data.frame(geno(all_vcf_PASS)$ADC[which(geno(all_vcf_PASS)$GT != '.', arr.ind=T...row.names=NULL)[1,]) > tumor_alt_support <- t(as.data.frame(geno(all_vcf_PASS)$ADT[which(geno(all_vcf_PASS)$GT != '.', arr.ind=T)],row.names...lt;-…

Cancer Cancer

updated 10.8 years ago • Sigve Nakken

here "B" to "C", thus samples without replicates). edgeR: countTable=read.table('mytable',header=F,row.names=1) ; dge <- DGEList(counts=countTable,group=c("A","A","A,"B","C")) ; dge <- calcNormFactors(dge) ; dge <- estimateCommonDisp(dge) ; dge...et <- exactTest(dge, pair=c("B","C")) or DESeq: countTable = read.table('mytable.csv', header=F,row.names=1) ; design = d…

edgeR DESeq edgeR DESeq

updated 12.3 years ago • Yvan Wenger

data frame with unique reads (raw) of all cells x <- x\[,c(g1,g2)\] x <- x\[!grepl("ERCC",row.names(x))&!grepl("Rn45s", row.names(x)),\] des <- data.frame(row.names=colnames(x),                 &nbsp

deseq2

updated 6.2 years ago • mdroog

Hi there! I am sending you this question because we've been using DESeq for some of the analysis that we usually perform and now we'd like to jump to DESeq2. We've been checking the DESeq2 manual but it is not clear to us how to switch from one version to the other. Could you please suggest what could be a proper way? DESeq is embedded in our pipeline and we'd like to add now version 2. Th…

Deseq2 Deseq

updated 9.8 years ago • Osvaldo

has 1 row, data has 0 In addition: Warning messages: 1: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames 2: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will...be forced to unique rownames 3: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames</pre> I've tried the same with…

seqcat

updated 6.3 years ago • omeally

<div class="preformatted">Hi all, I have millions like 100M DNA reads each of which is ~150nt, some of them are duplicate. Is there any way to group the same sequences into one and count the number, like unique() function in R, but with the occurrence...preformatted">Hi all, I have millions like 100M DNA reads each of which is ~150nt, some of them are duplicate. Is there any way to gro…

updated 14.3 years ago • Xiaohui Wu

to find DE gene. Based on limma manual, it reported time-course data, but not time-course data with duplication. So I wanna know that How to set function or parameters that build this correlation between time points in one

limma limma

updated 12.3 years ago • joseph

result? In my microarray experiment, I do biology repeat and technology repeat, every gene has duplicate in every microarray slide, so I will have 16 data points for each gene. If there is outliers, could I use limma to filter

Microarray limma Microarray limma

updated 19.7 years ago • ? ?