Bioconductor Forum

plot with no normalization for all arrays, but when I go to plot an M box plot with either within norm and or between normalization I get the following errors: Subscript out of bounds and then followed by "assign ("MAwithinArrays

Normalization GO limmaGUI Normalization GO limmaGUI

updated 20.5 years ago • Brooke-Powell, Elizabeth

for the same time point. conditions = c(__wt-treat,wt-untreat__,mut-treat,mut-untreat,__norm-treat,norm-untreat__,mock-treat,mock-untreat) I am a beginner in R so any help is appreciated. Thanks, Ruth

limma design matrix

updated 10.4 years ago • r.verstraten

value Can any one suggest me how is this possible Also how can i import mas.norm file for reading norm data

Mas5 normalization Exprs

updated 8.2 years ago • kritikamish99

offset=1) boxplot(as.data.frame(Enorm$E), main="Mean intensities - normexp") #Normalisation quantile NormE <- normalizeBetweenArrays(Enorm,method="quantile") boxplot(as.data.frame(NormE$E), main="Normalized intensities") pData...You need to check your .gpr files to find which signals you should extract. miRs <- c(grep("-miR-", NormE$genes$Name), grep("-let-", NormE$genes$Name)) Norm…

updated 14.4 years ago • bigoun

FALSE, quantile=0.9, groups =files$Group, verbose=TRUE) *s.norm <- normalizeCtData(raw.cat, norm="scale.rank")** **exprs(s.norm)** **write.table(exprs(s.norm),file="Ct norm scaling.txt")** ** **g.norm <- normalizeCtData(raw.cat, norm...geometric.mean")** **exprs(g.norm)** **write.table(exprs(g.norm),file="Ct norm media geometrica.txt")* Now if we look at the content of the two exp…

Normalization HTqPCR Normalization HTqPCR

updated 12.4 years ago • alessandro.guffanti@genomnia.com

lt;- dba.analyze(spik.model) #default lib size >dba.plotMA(spik.model, bNormalized = F, sub="No norm") >dba.plotMA(spik.model, bNormalized = T, sub="Norm: Lib size") >rm(spik.model) >spik.model <- dba.contrast(spik.counts...gt;spik.model <- dba.analyze(spik.model) >dba.plotMA(spik.model, bNormalized = T, sub="Norm: csaw bkgd bins RLE") >rm(…

DiffBind SpikeIn Normalization ChIP-seq csaw

updated 3.1 years ago • spg

the  <pre> cds <- calcNormFactors(cds, method = "none")</pre> Because It will bring the norm factor back to 1.. and I continue with calculating dispersion and doing the exact test. What is seems to me strange is that

edger

updated 7.3 years ago • Udi Landau

on the expression summary (using the loess method). I am not sure about how to do the latter (loess norm on the exp. summary). I have 2 conditions (say A and B) and triplicates (say A1, A2, A3 and B1, B2, B3). Once I get the expression summary

Normalization Normalization

updated 20.5 years ago • Emmanuel Levy

group (3 samples for each group). All is fine up to TMM normalization (I have understand how the norm factor are calculated) but starting from this point my nightmare start. I can't understand how my count matrix are used

edgeR glmQLFTest glmQLFit estimateDisp

updated 4.8 years ago • Giuseppe

by the failure of 4 of my samples (out of 44) to normalise. <pre> rawC<-MRcounts(bt[,p],norm=FALSE,log=TRUE) normC<-MRcounts(bt[,p],norm=TRUE,log=TRUE) plot(x=rawC,y=normC,main=p)</pre> If p is a 'good' sample I see a sensible

normalization metagenomeseq

updated 9.7 years ago • Stephen Rolfe

method = DBA_DESEQ2, normalize = DBA_NORM_RLE) #print out the normalization factors norm <- dba.normalize(CTCF_narrowpeaksnormalized, bRetrieve=TRUE) norm #contrast the read counts CTCF_narrowpeakscontrast

GenomicLocalization DESeq2 Cut&Run Diffbind Normalization

updated 5.1 years ago • Monica

I run the function AnalyzeTilingCelFiles. Does anybody know how to deal with this? Thanks!!!! > NORM <- AnalyzeTilingCelFiles(dir(pattern=".cel|.CEL"), "At35b_MR_v04-2_TIGRv5.bpmap", outfilename="normalizedata.tsv") [1] "Importing

AffyTiling AffyTiling

updated 16.0 years ago • zhen tao

normexp") > data\_norm <- normalizeBetweenArrays(data\_nobg,method="quantile") data\_ norm is in Elist class Now i would like to select the differentially expressed genes with creating a model.matrix and then

limma illumina microarray lmfit differential gene expression

updated 10.4 years ago • kanacska

NORM.data, factor = PHENO) BATCH.data <- ARSyNseq(BATCH.cor, factor="Group", batch = FALSE, norm = "n", logtransf = TRUE) to remove batch effect it separates the samples on PCA . But when is use varFilter(BATCH.data, var.func

DGE limma

updated 21 months ago • Amit

no normalization MA.q <- normalizeBetweenArrays(MA.p, method = "q") # quantile norm G.q <- normalizeBetweenArrays(RG.MA(MA.n)$G,method="q") # only green sc's # takes a matrix tmp<-cbind(RG.MA(MA.n)$R,RG.MA(MA.n...default p-loess MA.pq <- normalizeBetweenArrays(MA.p, method = "q") # pq norm MA.MpAq &am…

Genetics Normalization GO limma Genetics Normalization GO limma

updated 22.3 years ago • Natalie Thorne

files from an miRNA experiment. They are single color arrays, ( as opposed to 2 color as is the norm for GenePix I think). There is a subset of 7 arrays and I wish to compare a group of 4 of these to the other group of 3 and analyze

miRNA GO limma puma miRNA GO limma puma

updated 17.7 years ago • Paul Geeleher

problem is that when I go to plot an M box plot with any combination of normalization (either within norm and/or between slide normalization) I get the following errors: Error: subscript out of bounds Then Error in assign ("MAwithinArrays

Normalization GO limmaGUI ASSIGN Normalization GO limmaGUI ASSIGN

updated 20.4 years ago • Brooke-Powell, Elizabeth

correct to extract the fitted values for  visualization purposes to get rid of the noise. <pre> norm <-cpm(fit$fitted.values, normalized.lib.sizes = TRUE, log = TRUE, prior.count = 1)</pre> Issue 2. Is there any way to obtain only

edgeR cpm edger fitted model explained variance

updated 8.0 years ago • alakatos

I am correct that currently normalizeBetweenArrays will use all the values equally for whichever norm method is chosen? If so, could this option be added in the future? I think I can hack the scale part of the code for my own purposes

Normalization Normalization

updated 19.9 years ago • Jenny Drnevich

each run. My data includes 37 samples analyzed by EPIC array. All the analyses up to this level (QC, norm, SVD, DMP) went smoothly. This is the problematic line: myBlock <- champ.Block(beta=myNorm,pheno=myLoad$pd$Sample\_Group

champ champ.block

updated 8.1 years ago • tiroshamit

I am trying to compute some contrasts of interest and have three factors: Treatment (Hypoxic,Norm) Tissue (4 levels) Genotype (WT,KO) I chose a parameterization like this for the design matrix: > colnames(design) [1] "TSBrain.Hypoxic.KO

Kidney limma Kidney limma

updated 19.6 years ago • Sean Davis

and the code is working is excellent. But my question is after getting ouptut of *Cy.norm, cy.5 norm and log.ratio I want to calculate fold change among samples as my experiments has 3 samples and I want to see up and down

updated 15.4 years ago • ashwin Vishnuvardhana

of genes that don?t change. I get the following errors. > test2CLoess <- maNorm (test2Raw, norm = "loess", subset = nonDE, Mloc = TRUE, mscale = TRUE, echo = TRUE) Normalization method: loess. Normalizing array 1. Error in simpleLoess

Normalization limma marray Normalization limma marray

updated 21.2 years ago • M Inmaculada Barrasa

I have found how to use this normalize using an marrayraw object as argument ( e.g. maNorm(m, norm="median") ) but I can't seem to find how to do this with a matrix as argument. I have also tried the following but while my argument

Normalization Normalization

updated 13.2 years ago • Mark B

<div class="preformatted">Dear all, I am analysing qPCR data from the Exiqon where I have one card per sample, in each card I have one observation for each miRNA. I have in total 8 cards, 2 for treatment 1, 3 for treatment 2 and 3 for treatment 3. Each card has one endogenous gene, which I wouldn't like to use to normalize Ct values because is being affected by the type of treatment. So I …

miRNA qPCR miRNA qPCR

updated 15.0 years ago • Andreia Fonseca

to the comparisons listed above.  One of the follow-up goals was to look at reaction norms for DE genes from comparison one, looking for genes following a few specific patterns (basically constructing a generic...not examining interactions formally, and using this as a starting point to then look at the reaction norms.  I interpret this to mean that I should analyze the data in …

edger limma

updated 10.7 years ago • jbono

such that I'm unable to interpret this pattern. Is this to be expected? Am I doing something out of norm that results in this? Thank you very much. Volcano plot: https://ibb.co/JcMnK7r

edger scRNA-seq DGEA

updated 6.7 years ago • cronanz

<div class="preformatted">I have done this with all of the genes in a microarray experiment including blanks, negative controls, empties, hk genes, and spike ins, genes of interest 1. RG <- backgroundCorrect(RG, method="normexp", offset=50) 2. MA <- maNorm(as(RG, "marrayRaw"), norm="twoD") 3. WA <- normalizeBetweenArrays(as(MA, "MAList"), method="scale") This seems s…

Microarray Bayesian Microarray Bayesian

updated 15.9 years ago • stephen sefick

br/> Loading required package: IRanges<br/> Loading required package: GenomeInfoDb<br/> > ?norm<br/> ?norm                                             &nbsp

csaw edgeR chipseq

updated 10.1 years ago • gthm

any observation from other groups on this ? => data normalization: now normalizeCtData with norm="geometric.mean" supports the possibility of choosing the sample (the reference) which otherwise is by default the first...sample, as it is confirmed by themanual: > g.norm <- normalizeCtData(raw.cat, norm = "geometric.mean") Scaling Ct values Using geometric mean within each s…

Normalization HTqPCR Normalization HTqPCR

updated 12.2 years ago • alessandro.guffanti@genomnia.com

PC (GeneSpring apparently isn't very stable on anything else...LOL). I think I saw one to do an RMA norm of CEL files, and I'm not sure what else, but what I'm wondering is whether or not this is actually legal? If I'm a software developer

GO GeneSpring safe GO GeneSpring safe

updated 20.7 years ago • Ken Termiso

2:31], genes=rawdata[,1:1]) keep <- rowSums(cpm(y)>10) >= 15 y <- y[keep,] dim (y) #norm y <- calcNormFactors(y) #voom VST <- voom(y,design=NULL,plot=TRUE) voom_matrix <- cbind(VST$genes, VST$E) write.table (voom_matrix

Normalization Normalization

updated 11.8 years ago • Michael Breen

Mus_musculus/Ensembl/NCBIM37/Sequence/Bo wtie2Index/genome.fa --multi-read-correct --upper-quartile-norm --verbose accepted_hits.bam Cufflinks then names the chromosomes like this, is that correct? How can I control this or

updated 11.8 years ago • Sindre

div class="preformatted">Just a quick aside: > so I've been looking at 2D spatial norm Has anyone published using this method of normalisation? -----Original Message----- From: Christopher Wilkinson [mailto:Christopher.Wilkinson...the same thing. My bias is towards limma since I'm interested in the linear modelling approach (post norm) and limma is under active development (at least …

Microarray Preprocessing limma marray convert oligo Microarray Preprocessing limma marray

updated 22.0 years ago • michael watson IAH-C

rs } counts <- .rowsumAsMatrix(assays(se)[["counts"]], rowRanges(se)$cluster) norm <- .rowsumAsMatrix(assays(se)[["normalizedTpmMatrix"]], rowRanges(se)$cluster) SummarizedExperiment( rowRanges = consensus.clusters...SimpleList( counts = counts , normalized = norm)) }) ``` To solve this, `reord…

CAGEr

updated 3.1 years ago • Meng

<div class="preformatted"> Hi group, I'm trying to preprocess some two-colours single-channel slides. Looking through the mailing list archives I found some suggestions. But I still have some doubts... 1) first of all, a very basic question. In our group we came to the decision to simply don't consider the second channel (green) and to make all the work (BGcorrect, norm, etc) on the only…

updated 18.7 years ago • Giulio Di Giovanni

Hi list, We have recently seen an odd distribution of signal intensities using the new version 4 HT-12 chips. Specifically, the distribution of negative controls looks like a mixture of two gaussians. This invalidates the common assumption of normal distributed background used in both the detection calls and some error-model based normalizations, e.g. norm-exp in limma. We did not have this type…

limma neqc

updated 10.0 years ago • Arnar Flatberg

Load dataset using inSilicoDb eset21610 <- (getDataset("GSE21610", "GPL570", format = "CURESET", norm = "SCAN", features = "GENE")) \#Try to get rid of NA values eset21610$Heart\_Failure\[eset21610$Heart\_Failure == "NA"\] <- NA na.omit(pData

limma differential expression design matrix error eset

updated 10.5 years ago • Vani

This experiment was repeated and i have results of all these four experiment. Using Marray norm i could normalise the data and have exported M and A values on excel sheet. However, I need your suggestions to interpret

Microarray marray Microarray marray

updated 21.9 years ago • Binita Dutta

featureCategory (q)[!index,], and then no error happens. > q.norm <- normalizeCtData(sr.norm,norm="quantile") Warning messages: 1: In `[<-.factor`(`*tmp*`, ri, value = "normalizeCtData(q = sr.norm, norm = \"quantile\")") : invalid factor level...NAs generated 2: In `[<-.factor`(`*tmp*`, ri, value = "normalizeCtData(q = sr.norm, norm = \"quantile\")") : invalid fa…

HTqPCR HTqPCR

updated 14.9 years ago • Wenbo Mu

Gb="B532 Median"), wt.fun=f) pData <- data.frame(population = c('disease', 'disease', 'disease', 'norm', 'norm', 'norm')) rownames(pData) <- RG$targets$FileName design <- model.matrix (~factor(pData$population)) peptides<-grep("BAC1

limma limma

updated 15.6 years ago • K.Z.Nambiar@bsms.ac.uk

array experiment where I am compare 4 conditions: Wild-type (WT) versus Knock-out (KO) x Normal (NORM) versus Stress (STRESS). The hybs are replicated once (NNNNN_BLOCK1 and NNNNN_BLOCK2). I am most interested KOSTRESS-KONORM

limma limma

updated 19.2 years ago • Matthew Vaughn

color experiment. MA<-normalizeBetweenArrays(Rgene$G,method="quantile") design <- cbind(norm=1,normvstest=c(1,1,1,1,0,0,0,0)) fit <- lmFit(MA, design) fit <- eBayes(fit) topTable(fit, coef="normvstest", adjust="fdr") -- Regards, Abhilash

GO limma GO limma

updated 17.6 years ago • Abhilash Venu

priorImpact, . cyc = cyc, parallel = parallel, normType = > normType, normQu = normQu, . norm = norm, sizeFactor = > sizeFactor, quSizeFactor = quSizeFactor, . lowerThreshold = > lowerThreshold, upperThreshold = upperThreshold

cn.mops trimming

updated 2.8 years ago • yr542

priorImpact, cyc = cyc, parallel = parallel, normType = normType, normQu = normQu, norm = norm, lowerThreshold = lowerThreshold, upperThreshold = upperThreshold, minWidth = minWidth, segAlgorithm = segAlgorithm

cn.mops cn.mops

updated 10.5 years ago • Susan VanderPlas

a design and a DGEList object containing all the data, suitably anonymized. The DGEList already has norm factors and dispersions pre-calculated. The code demonstrates my method of selecting low-dispersion genes from 100...abundance bins and using them to recalculate the normalization factors. It then plots the old norm factors against the new ones and against the delta to see what effect there is…

Normalization GO limma edgeR Normalization GO limma edgeR

updated 12.5 years ago • Ryan C. Thompson

DATA .. X.mode <- normalizeGenome(X, normType="poisson") ### Parameter settings for tumor: ### - norm=0, because we already have normalized ### - integer copy numbers higher than 8 allowed ### - DNAcopy as segmentation algorithm...the position 2 is for NORMAL. ref_analysis_norm0 <- referencecn.mops(X.mode[,1], X.mode[,2], norm=0, I = c(0.025, 0.5, 1, 1.5, 2, 2.…

cn.mops

updated 8.7 years ago • Bogdan

subset" parameter of the maNorm function in marrayNorm? The documentation states: maNorm(mbatch, norm=c("printTipLoess", "none", "median", "loess", "twoD", "scalePrintTipMAD"), subset=TRUE, span=0.4, Mloc=TRUE, Mscale=TRUE, echo=FALSE, ...) subset

Normalization Normalization

updated 22.4 years ago • michael watson IAH-C

rowSums(cpm(raw) >= 1) >= 17) raw <- raw[keep, , keep.lib.sizes=FALSE] ## Normalization ## norm <- calcNormFactors(raw) ## DE analysis ## design <- model.matrix(~0+Cid+Group) colnames(design) design <- design[,-19] ed <- estimateDisp...norm, design) glmfit <- glmFit(ed, design) cont <- makeContrasts(Grouptreatment.V4…

edger

updated 7.0 years ago • candida.vaz

tmm". i execute NOISeq as: myresults <- noiseq(mytmmdata_a,mytmmdata_na,repl = "bio" , k=0.5 , norm="tmm" , long=1000, q=0.8, nss=0) My question is on the "q" parameter. Usually significant is when p.v = 0.05. What "q" value equal for that

NOISeq NOISeq

updated 13.8 years ago • Guest User

tips zraw.norm=maNormMain(zraw) ##Between slides normalization zraw.normg=maNormScale(zraw.norm,norm="g") ##And then the genefilter procedures, ## I want to flag the logratio(M) to NA according to the intensity of both channels of

Normalization probe genefilter Normalization probe genefilter

updated 20.7 years ago • Xiao Shi

<div class="preformatted">Dear All I have just seen a result which makes me either suspect the validity of print-tip loess normalisation, or wonder if there is a bug in bioconductor. I am performing print-tip loess normalisation on a dataset which I have already performed background correction on outside of bioconductor. Here is my code: > dataset[2896,1]@maRf chick1a_chick1.…

updated 21.6 years ago • michael watson IAH-C

Projects\\\\GAPPS Project\\\\GAPPS 2015 Neutrophils\\\\data and analysis\\\\fcs and compiled flowjo\\\\normed live export" >  > \#The flowCore method for reading in files > frames<-lapply(dir(folderPath, pattern = "\\\\.fcs",full.names...Projects\\\\GAPPS Project\\\\GAPPS 2015 Neutrophils\\\\data and analysis\\\\fcs and compiled flowjo\\\\normed li"…

flowCore flowcore CyToF Rtsne

updated 10.4 years ago • clevy

Loading required package: splines > rawdata = ReadAffy("GSM138562.CEL", "GSM138563.CEL") > norm = gcrma(rawdata) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment

cdf affy cdf affy

updated 18.6 years ago • Daniel Gatti

I am having trouble generating heatmaps and PCA plots after using the aggTax function in metagenomeSeq.  I receive the following error:   Error in hclustfun(distfun(x)) :    NA/NaN/Inf in foreign function call (arg 11)   Here is the code:   \#Aggregate data (using normalized counts); unaggregated data has 319 features and 69 samples; ag…

metagenomseq microbiome

updated 11.0 years ago • noelle.noyes

best algorithm to study genes at the low signal end on Affy chips. I have tried rma gcrma vsn (vsn norm, nbg, medianpolish) liwong mas5 To be honest, although mas5 is very noisy at low end, the real genes (the ones that I know are

affy gcrma affy gcrma

updated 22.1 years ago • Anthony Bosco

the same thing. My bias is towards limma since I'm interested in the linear modelling approach (post norm) and limma is under active development (at least more than I perceive marray is). Things I've used marray for is to get diagnostic...defined regions of very strong dye bias over 20-50% of the array) so I've been looking at 2D spatial norm and scale normalisation within array. With regards to…

Microarray Preprocessing limma marray convert oligo Microarray Preprocessing limma marray

updated 22.0 years ago • Christopher Wilkinson

<div class="preformatted">I am a newcomer to DNA microarrays and I have recently been playing around with the swirl dataset that is available through the bioconductor R package. I have seen some results regarding the swirl data set on the internet that have used one-sample empirical bayes moderated t-tests and the results seem to come out as expected (i.e. the most differentially expressed…

updated 21.6 years ago • Robert Cribbie

<div class="preformatted">Hello, I am trying out the quadrant and rangeGate methods in flowStats with a small sample of data. It seems that they do not play well with asinh transformed data when there is a small, but significant, population below zero. I have tuned the adjustable parameters sd, alpha and borderQuant as much as possible, but with less than ideal results. What I am looking f…

flowStats flowStats

updated 15.6 years ago • Aric Gregson

24 26 28 #mir.10 22 24 26 28 htNorm.gm = normalizeCtData(htData, norm = "geometric.mean") exprs(htNorm.gm); #Scaling Ct values # Using geometric mean within each sample # Scaling factors: 1.00 1.09...set.seed(1); exprs(htData.2) = exprs(htData.2) + runif(m) htNorm.sri = normalizeCtData(htData.2, norm = "scale.rankinvariant") head(exprs(htNorm.sri)) Furthermore…

Normalization HTqPCR Normalization HTqPCR

updated 11.5 years ago • Peter Langfelder