Bioconductor Forum

Probe 314 1942 41675 Notes on layout: ... > data.norm <- maNorm(data.raw,norm="loess",echo=TRUE) Normalization method: loess. Normalizing array 1. Error in if (is.int(totalPlate)) { : argument is of length

Normalization Biobase vsn limma marray Normalization Biobase vsn limma marray

updated 19.7 years ago • Nataliya Yeremenko

Probe 314 1942 41675 Notes on layout: ... > data.norm <- maNorm(data.raw,norm="loess",echo=TRUE) Normalization method: loess. Normalizing array 1. Error in if (is.int(totalPlate)) { : argument is of length

Normalization Biobase vsn limma marray convert Normalization Biobase vsn limma marray

updated 19.7 years ago • Nataliya Yeremenko

Hi everyone, I am investigating a CRISPR KO screen by modelling it as RNA-Seq data (I am aware that specialised tools for this exist e.g. MAGeCK, but am new to coding/R and am most familiar with DESeq2 for now), and it got me thinking about the ways in which we conduct differential analysis, and the differences between them. I first modelled the count data as usual using DESeq2, after exporting…

DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq

updated 20 months ago • james.zhang20

<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 14.6 years ago • Heidi Dvinge

say is correct, but the pseudo counts are not linearly related to counts-per-million, even when the norm factors are all 1. Their definition and purpose is described in Robinson and Smyth (Biostatistics, 2008). Pseudo counts...to the adjusted > library sizes. Since you have not used any normalization factors (i.e. > all norm factors = 1), the pseudo counts will simply be some const…

Normalization edgeR Normalization edgeR

updated 12.9 years ago • Gordon Smyth

4.508410<br/>             FoldChange DownS/Norm<br/> 211597_s_at             37.738164<br/> 211964_at   &nbsp...2.946915<br/> &nb…

limma deg

updated 8.8 years ago • nia

my .RDS file int R, but when I try to run **dba.plotHeatmap** i get an error: **Error in !pv$norm$DESeq2$bSubControl : invalid argument type** Does anyone know solution for this? Thanks Maja ```r sessionInfo( ) R version 4.1.2

DiffBind

updated 2.4 years ago • M.Vukic

in approach B but not in A? Should I nut be using same criteria? Thank you in advance! ``` #A1 norm by voom design=model.matrix(~Exposure + Line +sv1+ sv2+ sv3+sv4+ sv5, data = GenX_meta) dge.voom = voom(calcNormFactors(DGEList

Voom Limma WGCNA

updated 21 months ago • Gimena

<div class="preformatted">At 08:00 PM 31/05/2006, bioconductor-request at stat.math.ethz.ch wrote: >Date: Tue, 30 May 2006 14:13:04 -0400 >From: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> >Subject: Re: [BioC] Limma contrasts questions >To: Sean Davis <sdavis2 at="" mail.nih.gov=""> >Cc: Bioconductor <bioconductor at="" stat.math.e…

Kidney limma Kidney limma

updated 19.6 years ago • Gordon Smyth

which I know would be useful. I've provided the output from head() (see below). Apologies for other norms I might be breaking. Please call me out -- I'll do better next time. Thanks so much for any help.   Joe <pre> <strong>de_obj_TimeSeries

edge qpcr qvalue

updated 7.9 years ago • joe.d.moore.ii

<div class="preformatted">Dear BioC list, I have a strange error when I try to load flowQ on R 2.13.0. The installation went fine, with no errors but I am not able to load the library. My apologies if the error is been solved already, please be patient (! :-)), I could not find any solution on this list or on Google. This is the error when I load the library: > library(flowQ) Loadi…

flowQ flowQ

updated 9.2 years ago • René Dreos

it supports the use of both methods. But I’m worried that it is not too strong because the “CQN Norm>VST” curves are very flat. - As reported by <https: 95683="" p="" support.bioconductor.org=""></https:>, I also observed the GC-content

normalization CQN deseq2 RNA-seq network

updated 6.6 years ago • michael.pierrelee

backgroundCorrect(E, method="subtract") E <- backgroundCorrect(E, method="normexp", offset=50) NormE <- normalizeBetweenArrays(E, method="quantile") I don't understand you question about getting gene names in the toptable

Bayesian limma PROcess Bayesian limma PROcess

updated 15.4 years ago • Gordon Smyth

lt;- filterByExpr(y, group=y$samples$group) y <- y[keep, ,keep.lib.sizes=FALSE] #Calculate norm factors y <- calcNormFactors(y, method = "TMM") # Sample design matrix design <- model.matrix(~ 0 + Batch + Donor + Group) #Voom converts

edgeR contrastmatrix limma

updated 10 months ago • Elizabeth

F) h3k27ac <- dba.count(h3k27ac, bSubControl = F) #here the default score is library size norm #get raw counts h3k27ac <- dba.count(h3k27ac, peaks=NULL, score=DBA_SCORE_READS, bSubControl = F) h3k27ac_count_raw &lt

DiffBind

updated 3.6 years ago • ksong

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

Microarray Microarray

updated 11.4 years ago • Guest User

is now "dat"... > > Further i attach a boxplot (better than histogram right- "RMA vs Qunt > norm of MAS5 preproced & summed.jpg") comparing the two methods in my > orignal post. When i look at the variation of the RMA...processed and > normed data i question how effectively can i compare these arrays with > each. Especially along side the method s…

Microarray Normalization Preprocessing Cancer probe affy convert affyio Microarray Cancer

updated 19.4 years ago • James W. MacDonald

set.seed(1) DE_CUF_runLogCLR <- coseq(DEseq_DE_CUF_normalized, K=2:25, transformation="logclr",norm="none", meanFilterCutoff=10, model="kmeans", nstart=1, iter.max=15) ### **************************************** coseq analysis: kmeans approach & logclr transformation

coseq

updated 3.9 years ago • ajwijeratne1

<div class="preformatted">Dear Heidi, So I have each of my biological replicate in a plate, I have used the following command to read the data: > raw <- readCtData(files=files$File, path=path, n.features = 96, flag = 4, feature = 1, type = 2, position = 3, Ct = 5, header = FALSE, SDS = FALSE) my files: File Treatment 1 Emb1.txt Embrio 2 Emb2.txt Embrio 3 Emb3.…

miRNA qPCR Normalization limma miRNA qPCR Normalization limma

updated 15.7 years ago • Andreia Fonseca

Target" # Derive background data from normalized expression data bg <- derive_GeoMx_background(norm = nsclc@assayData$exprs_norm, probepool = fData(nsclc)$Module, negnames = c("NegProbe-CTP01", "NegProbe-Kilo")) # Load safeTME dataset

GeomxTools SpatialDecon GeoMxWorkflows

updated 16 months ago • Cinque

<div class="preformatted">I'm having some trouble getting FlowQ to load on my mac. Below is the attempt to load the package and some session info. I'mprobably missing something specific as all other packages are fine. library (flowQ) Loading required package: outliers Loading required package: mvoutlier Loading required package: compositions Loading required package: rgl Loading require…

flowQ flowQ

updated 14.4 years ago • Bennett, Brian

Hi, we're working on a data set from D. melanogaster and examining a series of TP of different knock-outs. we have several RNA-Seq data sets with triplicates. I was analyzing both the differences in each pair of time-points using DESeq2 as well as the time-series analysis using Mfuzz. I have tried to compare the expression values (or more precise profiles) created by Mfuzz and DESeq2 and got co…

deseq2 mfuzz differential expression timecourse

updated 9.3 years ago • Assa Yeroslaviz

<div class="preformatted">Fangxin, Yes it looks like the data is less than ideal. The last chip certainly looks dubious and should probably be repeated. I would definetely check with the experimenter how the samples were harvested and process and CONFIRM that they are true biological replicates. It's amazing how many lab plant biologists see pooled samples from a bulk of plants grown at th…

Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess

updated 20.0 years ago • Matthew Hannah

<div class="preformatted">Dear all, I am analyzing data of qPCR plates in which each well correponds to a miRNA. The system does not have replicates within the same plate. the data consistes in 3 types of cells: I have 3 replicates for cell type one; 2 replicates for cell type 2 and only one sampled cell type 3. The data of each cell type and each replicate is in a separate file where the …

miRNA qPCR miRNA qPCR

updated 15.3 years ago • Andreia Fonseca

tumor_normal_count_loess_blacklisted, offsets = TRUE) norm <- dba.normalize(tumor_normal_normalized_loess_blacklisted, bRetrieve = TRUE) norm # ============ Modeling and contrast ================ tumor_normal_contrasted_loess_blacklisted

DiffBind Normalization

updated 21 months ago • Henry

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

Normalization marray convert Normalization marray convert

updated 19.2 years ago • Gordon Smyth

<div class="preformatted">Aha! Thanks for the tip - am getting gene names now! And thanks for the look-see at my script. Cheers, Lisa -A couple of corrections. Background correct is yet doing everything it -should with EList objects, so the background subtraction has to be done -manually. And I now see why you're not getting gene names in your -toptable. You can use - - x <- …

Annotation Bayesian limma PROcess Annotation Bayesian limma PROcess

updated 15.4 years ago • Orfe, Lisa

Hi all, I have an experiment with 28 human samples spread over 2 experimental batches. One variable of interest, trt, and 6 other possible variables: expt, sex, age, race, smoker\_yrs and cigs\_week. The question is how to pick which variables to include in the model when different genes may show different effects of the variables? Instead of trying to pick one best model for all genes, I had th…

WGCNA limma voom

updated 9.3 years ago • Jenny Drnevich

5) 22 rbind(deparse.level, ..1, ..2, ..3, ..4, ..5, ..6, ..7) 23 normalizeCtData(q = raw_monster2, norm = "deltaCt", deltaCt.genes = "GAPDH") 24 filterCtDataNew(q = d.raw2, remove.type = "Endogenous Control") 25 setCategory(q = fd.raw2

HTqPCR HTqPCR

updated 15.5 years ago • Bass, Kevin

statistical testing is invalid. > > >> I find hist, RNA deg, AffyPLM and a simple RMA norm followed by > >> plot(as.data.frame(exprs(eset.rma))) can answer in most cases for why it > >> didn't work, or won't work

Normalization probe affy affyPLM Normalization probe affy affyPLM

updated 20.0 years ago • Naomi Altman

have ~50 samples that have been run on both arrays, and if these pairs cluster closely post-join and norm I hope to combine data from these arrays for an EWAS Any help or insight in moving forward would be greatly appreciated

EPICV1 Methylation combineArrays minifi EPICv2manifest

updated 21 months ago • Kim

samplesheet). I am getting the exact same Pvalues for all three methods. I did check that the `DBA$norm$DESeq2$norm.facs` values are different in each case. The MA plot using normalized counts also does not seem to be consistent

DiffBind

updated 22 months ago • red_bricks

<div class="preformatted">When I try to open some FCS files using iFlow, I get several strange error messages, and I am ultimately unable to open the files.... In iFlow, I get a pop-up box that says "Warning: 'signed = FALSE' is only valid for integers of sizes 1 and 2." In the R console, there are some warnings about RGtk2 'method' being deprecated - how can I clear this? When I try to o…

GUI iFlow GUI iFlow

updated 13.9 years ago • Gabriel Nathan Kaufman, Mr

comptb)<-paste("brut.",rownames(coldatafile),sep="") comptn<-as.data.frame(counts(dds3,norm=TRUE)) colnames(comptn)<-paste("norm.",rownames(coldatafile),sep="") compt<-merge(comptb,comptn,by.x=0,by.y=0) rownames(compt

deseq2

updated 9.5 years ago • cagenet34

gnames = genes, layout = >layout, targets = maTargets, header=F) > >maN <- maNorm(ma, norm="p") > >lmset <- maM(maN) Have you checked that you have actually read in the data at this stage, e.g., summary(lmset)? >lmser

Microarray limma Microarray limma

updated 22.5 years ago • Gordon Smyth

gt; y <- y[keep, , keep.lib.sizes=FALSE] > > ## ----norm------------------------------------------------------------------ > y <- calcNormFactors(y) > > ## ----estimateDisp---------------------------------------------------------- > y <- estimateDisp(y, design, robust=TRUE) > > ## ----glmQLFit-----------------…

edgeR prior.count

updated 7.2 years ago • Jenny Drnevich

I am running  R version 3.1.2 and launched champ.process() using the default command in the documentation as a first attempt. All the proper .cvs and iDat files are presumably in the home folder. The command is accepted, the output folder is created, and the two .cvs files are read in when all of a sudden the program returns "Killed" and R quits; I find myself at the unix promp…

champ

updated 11.1 years ago • schasse

<div class="preformatted">Hi Fran?ois, Please don't take emails off the list (I've re-copied the list here). Also, this document may help you: http://bioconductor.org/help/mailing-list/posting-guide/ > Could you confirm (or not) what I am saying here? Unfortunately, I haven't been able to decode what you are doing or are trying to do. I've added a couple comments and suggestions …

Normalization edgeR Normalization edgeR

updated 13.5 years ago • Mark Robinson

gt; y <- y[keep, , keep.lib.sizes=FALSE] > > ## ----norm---------------------------------------------------------------- > y <- calcNormFactors(y) > > > ## ----design-------------------------------------------------------------- > design <- model.matrix(~0+group) > colnames(design) <- levels(group) &am…

limma edgeR

updated 8.5 years ago • Jenny Drnevich

filtering the dds and i see the same thing.  I have also checked (several times) import of the norm'd read and avg fpkm values, so no mistake there. Finally, exploratory analysis of this dataset shows that there is a HUGE...resultsNames(dds) counts\_norm <- counts(dds,normalized=TRUE) write.table(counts\_norm,file="normed\_counts.txt",row.names=TRUE,col.names=TRUE,quote=FALSE,s…

deseq2

updated 8.1 years ago • wlorenz

both conditions! I've checked everything I can think of... I don't get any errors or warnings, the Norm Factors are sensible, the raw signal is sensible, all the objects look well-formed (i.e. like they contain all the bits they

Normalization edgeR Normalization edgeR

updated 14.3 years ago • Nick Schurch

<div class="preformatted">Dear Paul, The limma User's Guide doesn't discuss how to read single channel data, but how to do this has been described half a dozen times on this mailing list. Since limma is designed for two colours, you can fool it by giving two column names and ignoring the one you don't need. If you only have the Cy3 channel foreground for example you might use Cy3 &am…

miRNA Microarray Normalization GO limma miRNA Microarray Normalization GO limma

updated 17.7 years ago • Gordon Smyth

them > on arrays. I use GenomeStudio to output summarized beadtype values (no bg or > norm), and GenomeStudio always re-organizes the by Sample_Group. I've learned > to double-check that the order in my targets

Microarray GO limma Microarray GO limma

updated 14.6 years ago • Gordon Smyth

conditions! I've checked everything I > can think of... I don't get any errors or warnings, the Norm Factors are > sensible, the raw signal is sensible, all the objects look well- formed > (i.e. like they contain all the bits

Normalization edgeR Normalization edgeR

updated 14.3 years ago • Gordon Smyth

gl <- t(t(gl)-colMeans(gl)) >> >>> >> >>> # Combine library sizes, norm factors and gene lengths: >> >>> >> >>> offset <- expandAsMatrix(getOffset(y)) >> >>> offset <- offset

RNASeq Normalization Organism zebrafish edgeR

updated 11.4 years ago • assaf www

0 0 0 0 0 0 14 15 27 1 1 2 2 > >> q.norm <- normalizeCtData(raw.cat, norm="quantile") > >> qDE.ttest <- ttestCtData(q.norm[,1:99], groups=files$Treatment[1:99], > > + calibrator="Normal") > >> qDE.ttest...0 1 0 0 14 45 15 27 1 1 2 2 0 > >> q.norm…

Cancer ddCt cycle HTqPCR ASSIGN Cancer ddCt cycle HTqPCR ASSIGN

updated 14.3 years ago • Heidi Dvinge

<div class="preformatted">Hi Gordon, Thanks for the quick response, and sorry I didn't get back to you yesterday. I'll try to address each of your questions clearly. 1) >> Finally, would you be willing to share some of your date with us offline so that we can >> trouble-shoot? As I said, we haven't seen this behaviour. We'd be happy to share the anonymized d…

Normalization limma edgeR DESeq Normalization limma edgeR DESeq

updated 14.3 years ago • Nick Schurch

Bioconductors: We are pleased to announce Bioconductor 2.13, consisting of 749 software packages, 179 experiment data packages, and more than 690 up-to-date annotation packages. There are 84 new software packages, and many updates and improvements to existing packages; Bioconductor 2.13 is compatible with R 3.0.2, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release in…

BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage

updated 12.3 years ago • Dan Tenenbaum

Hey Mark, I had a self-made file, but this one would also be fine if it worked. This time, this happened: > txdb <- makeTranscriptDbFromGFF(file="NC_008463_ncbi.gff", format="gff3", dataSource="CDS", species="Pseudomonas aeruginosa", chrominfo=inf) extracting transcript information Error in .prepareGFF3TXS(data) : No Transcript information present in gff file > sessionInfo() R versio…

Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD

updated 12.4 years ago • Sarah Pohl

Bioconductors: We are pleased to announce Bioconductor 2.12, consisting of 671 software packages and more than 675 up-to-date annotation packages. There are 65 new software packages, and many updates and improvements to existing packages; Bioconductor 2.12 is compatible with R 3.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS X. This release includes an updated Bioconductor Ama…

BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO

updated 10.5 years ago • Dan Tenenbaum