Bioconductor Forum

24.0"), pAdjustMethod = "fdr") res <- res[order(res$padj), ] export(res, desc, counts, norm, "24.3", "24.0", "f1", "genes_24_0_3") res <- results(dds.skin, contrast=c("f1", "24.6", "24.0"), pAdjustMethod = "fdr") res <- res[order(res$padj...export(res, desc, counts, norm, "24.6", "24.0", "f1", "genes_24_0_6") res <- results(dds.…

deseq2

updated 10.2 years ago • carleshf

<div class="preformatted">Hello all, We are having a problem analyzing a large data set (30 Affy soybean arrays, ~61K probesets). I moved from my PC to our server running IRIX, but I'm still getting the same error message of "unable to allocate vector size...". There are 12 G of physical memory on the server plus another 17 G swap; the R process doesn't even touch a fraction of this, so it…

cdf reposTools affy cdf reposTools affy

updated 20.3 years ago • Jenny Drnevich

know! Best, ~Lina <pre> > mydatacorr1 = ARSyNseq(mydata, factor = "date", batch = TRUE, norm = "tmm", logtransf = FALSE) Error in if (all(obs == ref)) return(1) : missing value where TRUE/FALSE needed > mydata ExpressionSet (storageMode

noiseq batch effect ARSyNseq

updated 10.2 years ago • lina.faller

<div class="preformatted"> I use Limma Dev. Package and i'd like output my normalized data, but i have a problem: > library(limma) > library(sma) >YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\t" ,as.is=TRUE) > YourSample SlideNamber FileNameCy3 FileNameCy5 Cy3 Cy5 1 1 slide1_1_Cy3.txt slide1_0_Cy5.tx…

limma limma

updated 22.1 years ago • utepandragon@tiscali.it

combined data (CPM) and another method, I normalized (CPM) the data separately then combined the log norm. I haven't tried to calculate log2FC yet so far. My question is, what is the most appropriate strategy to combine 2 different

deseq2 normalization probe

updated 5.8 years ago • l.s.wijaya

Next I tried an overall loess normalisation on housekeeping genes exp48.norm<-maNorm(exp48, norm="loess", subset=(housekeep ==1)) and while maPlot(), maDiagnPlots1(), maNormPlots(), work fine (if I'm careful about graphics window

updated 23.4 years ago • Peter Baker CMIS, Indooroopilly

0+groups) colnames(design) = levels(groups) nf <- calcNormFactors(dat.spike.in) # calculation norm factors using spike ins only voom.norm <- voom(dat.without.spike.in, design, lib.size = colSums(dat.spike.in) * nf) # add

limma voom deseq normalization ercc

updated 10.1 years ago • komal.rathi

e.g. for the rest of my data analysis I use CSS, see here: [http://www.metagenomics.wiki/tools/16s/norm/css][2], but I can't figure out how to use a normalized data frame as input to the DESeq (it asks always for this size factor estimate...1]: https://github.com/joey711/phyloseq/issues/1424 [2]: http://www.metagenomics.wiki/tools/16s/norm/css

DESeq2

updated 5.0 years ago • Mathilde

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

Normalization GO limmaGUI ASSIGN Normalization GO limmaGUI ASSIGN

updated 20.4 years ago • Gordon Smyth

gt; 2) >= 2 d <- d0[keep, , keep.lib.sizes=FALSE] dim(d) #29089 genes remaining #Calculate norm factors after filtering. dt <- calcNormFactors(d) dt$samples dgex2 <- estimateCommonDisp(dt, verbose=TRUE) degxplot2...4 4 4 mmg <- model.matrix(~group) ydt <- voom(dt, mmg, plot = T) #norm factors calculated on filtered data #test model…

limmavoom filtering edgeR RNASeqData meanvariancetrend

updated 12 months ago • gingergeiger22

border="0" src="https://i.ibb.co/X44rCPB/noShrink.png"/></a> <a href="https://imgbb.com/"><img alt="norm-Shrink" border="0" src="https://i.ibb.co/1R554sC/norm-Shrink.png"/></a> <a href="https://imgbb.com/"><img alt="ashr-Shrink" border="0" src="https

deseq2 ashr rna-seq

updated 5.7 years ago • Alex

<div class="preformatted">At 09:15 AM 1/02/2006, Jenny Drnevich wrote: >Hello all, > >It appears that normalizeWithinArrays by default takes the weights >in an RGList into account when doing a normalization, but this does >not appear to be an option for normalizeBetweenArrays. Yes. > I am correct that currently normalizeBetweenArrays will use all…

Normalization Normalization

updated 19.9 years ago • Gordon Smyth

lt;- samples data$totals <- libsizes data <- normOffsets(data, method="loess", se.out=TRUE) norm <- estimateDisp(asDGEList(data), design) result <- glmQLFTest(glmQLFit(norm, design, robust=TRUE)) table(sign(result$table

diffHic

updated 4.5 years ago • arielpaulson

tumorFactor) mod0 <- model.matrix(~ 1, svaInfo) svseq <- svaseq(as.matrix(norm\_EDA\[use,\]), design, mod0) SV1 <- svseq$sv\[,1\] SV2 <- svseq$sv\[,2\] dds\_sva <- DESeq2::DESeqDataSetFromMatrix(countData =round(dat

sva paired samples rnaseq

updated 9.6 years ago • gumilton

of an affymetrix study. I have 8 samples (in duplicate) and 3 factors. The factors are O2 level (Norm, Hypo), Radiation (Yes/No) and Treatment (None, DMSO, Drug1, Drug2). The drugs were delivered to the cells using DMSO as a carrier

limma limma

updated 15.6 years ago • Iain Gallagher

between species. Any help would be greatly appreciated. [1]: https://i.ibb.co/rpd9q6z/norm-counts.png

deseq2

updated 5.4 years ago • fl

data <- gpTools(raw=TRUE) > data <- gpTools(raw=TRUE) [1] NA [1] "Reading ./Sr90 5K A total norm 10%.gpr" Error in readLines(con, n, ok) : invalid value for `n' Investigating this further, I have found that the .gpr files I am using

Microarray Microarray

updated 21.8 years ago • McKinstry, Craig A

tumor_normal_count_loess_blacklisted, offsets = TRUE) norm <- dba.normalize(tumor_normal_normalized_loess_blacklisted, bRetrieve = TRUE) ``` ```r > norm $norm.method [1] "adjust offsets

DiffBind

updated 21 months ago • Henry

<div class="preformatted">> Message: 6 > Date: Thu, 29 Jan 2004 09:17:31 -0000 > From: "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> > Subject: RE: [BioC] Re: [Fwd: Bioc Book Chapter] (Gordon K Smyth) > Biocondu ctor Digest, Vol 11, Issue 38 > To: bioconductor@stat.math.ethz.ch > > Just a quick aside: &gt…

Microarray Normalization Microarray Normalization

updated 22.0 years ago • Christopher Wilkinson

from the first sample! The code I am executing is as follows: countdata<-read.csv(file = "non-norm\_counts.csv") countdata1<-countdata\[,-1\] rownames(countdata1)<-countdata1\[, 1\] I get the following error:  duplicate

deseq2 countdata

updated 7.9 years ago • A

trait (continuous)   Several questions on this topic:  1. If I extract the norm counts from deseq and run the same regressions (negative binomial) myself, the results don't match the deseq LRT results

deseq2 negative binomial model robust regression sleuth

updated 8.6 years ago • stoyo_karamihalev

FALSE] the library sizes are recalculated, right? ``` dge.n <- calcNormFactors(dge) # Calc norm factors design <- model.matrix( ~ groups) colnames(design) <- c("basal", "her2", "luma", "lumb") # change colnames of design matrix head

edgeR anova rna-seq

updated 4.7 years ago • Antonio M.

gt; res <- results(dds, independentFiltering=FALSE) > run <- coseq(counts(dds, norm=TRUE)[which(res$padj < 0.05),], + normFactors = "DESeq", transformation = "logclr", + model = "kmeans", parallel = TRUE, meanFilterCutoff

coseq RNAseq clustering

updated 6.0 years ago • minyaaa9058

qPCRnew,remove.category="Undetermined" ,n.category=1) #normalized q2.NORM= normalizeCtData( q2.cat,norm="deltaCt",deltaCt.genes=c("ABL1-Hs01104728_m1","MRPL19-Hs0 1040217_m1","HPRT1-Hs03929098_m1")) ######limma design <- model.matrix

ddCt HTqPCR ddCt HTqPCR

updated 14.0 years ago • marco fabbri

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&lt

limma limma

updated 15.6 years ago • Gordon Smyth

Hi there! I am currently using DiffBind v3.2.7 to analyse some ChIP-seq data for RNA Polymerase III (RNAPIII). We have Drosophila spike-in chromatin in the samples that I would like to use in DiffBind to normalise the data. The problem is that during library prep, some of the samples accidentally got different proportions of the spike-in chromatin relative to sample chromatin. My question…

DiffBind ChIPSeq Normalization SpikeIn

updated 4.3 years ago • Drew

error, not due to gene expression. ... And good luck! You may also find help on the microarray-norm@ebi.ac.uk mailing list Thanks Mick</div

Sequencing GO Sequencing GO

updated 21.4 years ago • michael watson IAH-C

1]) updateCelUnits(pathname, cdf=NULL, intens) and checked my variables- > pathname [1] "L:/Normed data/CIR_5-D-309.CEL" > intens[1:4] $`129981` [1] 7.566183 $`212118` [1] 8.783549 $`393384` [1] 8.812677 $`84268` [1] 10.39683 However, when

Microarray hgu133a2 affxparser Microarray hgu133a2 affxparser

updated 14.5 years ago • Martha Behnke

processing? what is setting? > normalizedMatrix <- MRcounts(root_data, norm = TRUE) > settings = zigControl(maxit = 1, verbose = FALSE) Is it correct way to make model matrix? > mod = model.matrix(~root_data

limma metagenomeSeq

updated 6.6 years ago • nabiyogesh

Peaks="PeakNormFactors", HiAb="HANormFactors") %>% ## (CALCULATION OF NORM FACTOR LINE HEIGHTS HAPPENS HERE) sapply(. %>% colData(window.counts)[[.]] %>% log2 %>% {.[s2] - .[s1]}) %>% data.frame(NormFactor=., NormType...data=linedata, aes(yintercept=NormFactor, color=NormType)) + scale_color_discrete(name="N…

csaw normalization

updated 9.7 years ago • Ryan C. Thompson

exp). It is in the form of a data frame called "all." I did not do any other filtering or scaling or norm other than a simple call to rma(). I then transposed the data frame so that its dim are 8 x 22283, and called that "allt." allt.som

affy affy

updated 20.6 years ago • Ken Termiso

<div class="preformatted">Hi Arnar, Wei Shi and I have checked out our own HT-12 v4 data, and we do not see the bimodal distribution that you have observed. So we think that this might be a property of your data rather than a property of HT-12 v4 BeadChips in general. Note that we are now recommending the neqc() function of the limma package for background correcting and normalizing Illu…

limma limma

updated 14.9 years ago • Gordon Smyth

td> <td>2 hr</td> <td>2 hr</td> <td>2 hr</td> <td>2 hr</td> <td> </td> </tr> <tr> <td>Gene A norm cts</td> <td>100</td> <td>110</td> <td>100</td> <td>150</td> <td>300</td> <td>350</td> <td>400</td> <td>320</td&…

normalized counts log2

updated 7.3 years ago • agdif

CN7","CN8","CN16","CN32","CN64","CN128"), priorImpact = 1, cyc = 20, parallel = 0, norm = 0, normType = "poisson", sizeFactor = "mean", normQu = 0.25, quSizeFactor = 0.75, upperThreshold = 0.5, lowerThreshold = -0.9, minWidth...CN7","CN8","CN16","CN32","CN64","CN128"), + priorImpact = 1, cyc = 20, parallel = 0, norm = 0, …

cn.mops

updated 9.4 years ago • Mohammad Alkhamis

RG,layout,pch=16,cex=0.1,image=3) > > plot.print.tip.lowess(RG,layout,pch=16,cex=0.1,image=3,norm="p") > > MAraw <- MA.RG(RG) > >plot.scale.box(MAraw$M[,3],layout,col=rainbow(layout$ngrid.r*layout $ngrid > .c)) > > abline

limma limma

updated 22.1 years ago • Gordon Smyth

www.bioconductor.org=""> e.g. filtered lowly expressed genes, normalised gene distributions (Calc Norm Factors with method="TMM") Then proceeded to the dream vignette <https: bioc="" devel="" doc="" dream.html="" inst="" packages="" variancepartition

RNAseq variancePartition edgeR dream

updated 2.8 years ago • DH

maxcnt = maxcnt, legend = 1, lcex = 1, newpage = FALSE) 2: qpHexbin(mnorm, main = "MA-Plot :: Norm") 1: maQualityPlots(data.raw) But then I used the trace function to edit the qpHexbin function to plot using gplot.hexbin

updated 11.4 years ago • Guest User

Rf_label, name.Rb = Rb_label) A print tip-loess normalization for every slide: gn <- maNorm(g, norm="p") Then comes the normalization between arrays. I use the "normalizeBetweenArrays" command here. I basically just copied

Normalization Normalization

updated 19.2 years ago • Michael Nuhn

<span style="line-height:1.6">I have sequences 96 samples, 48 from tumor and 48 from normal tissue. I want to check if the miRNAs in the tumor samples are globally down-regulated compared to normal samples. I was thinking of comparing the median expression of all the tumor libraries to the median of all the normal libraries. </span> What kind of normalization do I need to do…

edger limma mirna sequencing

updated 10.5 years ago • R

had used it), so I am eager to have inputs/guidelines about when to decide using TMM vs quantile norm. Input on this most welcome! Thanks! Jean-Marc

limma voom limma voom rna-seq quantile normalization

updated 9.9 years ago • lassancejm

fn2sp)) \# co __\#I've found this for reading cell file__ affyGeneFS <- read.celfiles(raw) norm <- rma(affyGeneFS, target = "probeset") Background correcting Normalizing Calculating Expression Warning message: 'isIdCurrent...I get these message, or if i can continue working then it can stay like that???__ expr<- exprs(norm) __AFTER THIS STEP CAN I USE limm…

microarray annotation hgu133plus2 hugene20

updated 10.8 years ago • kanacska

gt; class(affyRaw) \[1\] "HTAFeatureSet" attr(,"package") \[1\] "oligoClasses" > norm<-rma(affyRaw, target="probeset") Error in (function (classes, fdef, mtable)  :    unable to find an inherited method...for function ‘probeNames’ for signature ‘"HTAFeatureSet"’ >norm<-rma(affyRaw, target="core") Error in (function (classes,…

affymetrix microarrays microarray pd.hta.2.0 oligo rma

updated 9.8 years ago • jennifer.drake

only the probes expressed in ALL samples = ~8500 probes However with lumi: raw = lumiR("file.txt") norm = lumiExpresso(norm,QC.evaluation=TRUE) x = exprs(norm) presentCount = detectionCall(x) y = x[presentCount > 0,] =~20,000 When I compared

probe limma lumi probe limma lumi

updated 15.0 years ago • Jovana Maksimovic

had gene symbol /ID as "NA". Ended up with 34886 probe ids (Started with 70k probes after core rma norm). 8- set up design matrix - I would like to look at a list of differential expressed gene based on treatment and time effect

limma hta affy annotation

updated 6.8 years ago • RV

bamimportParams <- setImportParams( offset = -1, fix_width = 0, fix_point = "start", norm = TRUE, useScore = FALSE, outRle = TRUE, useSizeFactor = FALSE, genome = "mm39" ) plot_5parts_metagene( queryFiles = queryfiles, gFeatures_list

GenomicPlot

updated 15 months ago • Lucky

Enter the body of text here Hi All, I need some urgent help regrading pca analysis to show the clustering of my 13 samples based on treatment condition. I have run the code and generated a biplot which is showing the 13 points represent 13 samples but the problem is I want to draw an ellipse for 2/3 replicates under the same treatment. How can i do that? Could anyone help me in this regards?…

Biplot FactoMineR proteomics PCAtools ellipse

updated 3.0 years ago • M Tuhin

<div class="preformatted">Hi Mark, On 10/27/2012 5:13 PM, Mark B wrote: > Hi, > I am trying to normalize a matrix of logged (base 2) cDNA expression > intensity values (dimensions 4000, 4) from only the Cy5 channel derrived > from an marrayraw object. I would like to normalize the values > using global median normalization where all arrays result having…

Normalization GO Normalization GO

updated 13.2 years ago • James W. MacDonald

Hello, I am trying to generate a qDE.limma file for subsequent analysis and visual representation. Strangely, I lose my gene names after running the limmaCtData function. Am I doing something wrong? <pre> raw <- readCtData(files = "1131361180.csv", path = path, format = "BioMark", n.features =48, n.data = 48) raw.D1filt <- raw[, c(1,2,4,5,7,10,13,16,17,20,23,25,26,28,31,…

limma htqpcr

updated 10.4 years ago • julio.c.silver

age <- target$Age sex <- as.factor(target$Sex) dx <- relevel(factor(target$dx), ref="Norm") #Norm, MCI, Dem batch <- factor(target$batch) #(denoted as 1,2,3)</pre> \#\#\#\#\#\#\# <pre> all(target$array_ID==colnames(y_29)) #TRUE</pre> \#\#\#Analysis with

illumina human ht-12 v4 limma pipeline

updated 9.4 years ago • alakatos

relationship final dispersion estimates fitting model and testing > counts <- counts(dds,norm=TRUE) > counts <- as.data.frame(counts) > res <- results(dds) > markers <- res[abs(res$log2FoldChange)>2 & res$padj...relationship final dispersion estimates fitting model and testing > counts2 <- counts(dds2,no…

kallisto deseq2 tximport

updated 8.2 years ago • thibault.lorin34

<div class="preformatted">I hope someone can help me with a strange problem with affy hgu133a2. I have an affy array with minimum signal and 1st Qu. signal equal zero, but it seems OK from the RPT file from GCOS: >all.raw1 AffyBatch object size of arrays=732x732 features (4191 kb) cdf=HG-U133A_2 (22277 affyids) number of samples=1 number of genes=22277 annotation=hgu133a2 >…

hgu133a2 probe affy hgu133a2 probe affy

updated 19.9 years ago • Dick Beyer

<div class="preformatted">Hi Chris, we have seen the same phenomenon with affyRNA degradation plots. There is definitely a smooth trend, until the last point. It is very reproducible, in fact this position should show the highest intensity overall, but shows about 50% of what would be expected. Best, Mark -----Original Message----- From: bioconductor-request@stat.math.ethz.ch [mailto:bioc…

Microarray Normalization Cancer probe ROC limma PROcess Microarray Normalization Cancer

updated 22.4 years ago • Vawter, Marquis

does not contain column Raw_intensity (choose other type instead)</pre>   And with type = "Norm" <pre> Error in .readCodelinkRaw(files = filename, ...) : File /media/hussain/A006D86A06D84348/data/GSE59907_RAW/GSM1453331_T00141653_2002

codelink

updated 7.8 years ago • Agaz Hussain Wani

X.norm <-normalizeGenome(XRanges) resRef3 <- referencecn.mops (X.norm[,1:4], X.norm[,5:8],norm=FALSE) Best regards, Günter -- Günter Klambauer Institute of Bioinformatics Johannes Kepler University, Linz, Austria

updated 11.9 years ago • Günter Klambauer

_obj\_file\_aband\_graph, lvl='Class', feature = "c\_\_Clostridia",id="X.SampleID", time="Age", B=10, norm=F, log=F) Error in sort.list(y) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a list? Could someone tell me what is going

metagenomeseq fittimeseries

updated 9.2 years ago • wijera81

<div class="preformatted"> I would like to analyse my sequencing data with anota, starting with the function "anotaPerformQc". Regrettably I get the following error message: anotaQcOut <- anotaPerformQc(dataT= my_data_cytosolic_mRNA, dataP=my_data_translational_Activity, phenoVec=vec, nDfbSimData=500, useProgBar=TRUE) Running anotaPerformQc quality control Calculating omni…

Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota

updated 10.4 years ago • Guest User

<div class="preformatted"> Greetings friends! I seek help with data that I have : 3 time points, 3 genotypes, 3 replicates for each of these = 27 libraries The goal is to find genes that have different time expression profiles amongst 2 or more genotypes. After our 1st round of data analysis, (including TMM normalization), the time course graphs and box plots were so noisy in terms of hi…

Normalization edgeR Normalization edgeR

updated 13.3 years ago • Guest User

or "thresholds". <span style="line-height:1.6">I have tried to change the parameter of  "norm", "priorImpact", "segAlgorithm", "lowerThreshold" or "upperThreshold". Sometime it works, and sometime it doesn't.</span> <span

No CNVs detected. Try changing "normalization" "priorImpact" or "thresholds". cn.mops

updated 9.3 years ago • Ponyo

toptable? limma computes generalized least squares, using any weights which it finds in your object 'norm' and taking into account the correlations between duplicates. It is not a simple average, nor even a simple weighted average

limma DOSE limma DOSE

updated 20.9 years ago • Gordon Smyth

10 2.418771e-06 12.80131 > dir() [1] "array image K562 Lucena sem VCR.jpeg" [2] "Box plot norm data histogram.jpeg" [3] "Box plot raw data histogram.jpeg" [4] "K562 1.CEL" [5] "K562 2_1.CEL" [6] "K562 vs Lucena-VCR" [7] "limma_completeK562...vs Lucena.xls" [8] "Lucena sem VCR 1.CEL" [9] "Lucena sem VCR 2.CEL" [10] "MAplot Norm data.jpeg" [11] "MAplot Raw data.jpeg" [1…

graph SPIA graph SPIA

updated 15.8 years ago • Marcos Pinho