230 results • Page 1 of 4
else asks.... ;-) ... subscription to a variety of useful mailing lists, including microarray-norm@ebi.ac.uk, is available here http://www.mged.org/Workgroups/index.html In fact, there's a whole host of useful stuff on
updated 21.8 years ago • michael watson IAH-C
Any help or suggestions would be greatly appreciated! Thanks so much, Norm Norm Allaire Scientist II Genetics and Genomics Biogen Idec 14 Cambridge Center Cambridge, MA 02142 Office: 617-679-2932
updated 11.9 years ago • Norm Allaire
<div class="preformatted">Hi, I'm new to R. I'm trying to analyze 8 Fluidgm 96 *96 plates (96 assays and 192 samples replicated 4 times). I downloaded and installed HTqPCR and I'm now trying to read in the raw data. I am using the "HTqPCR -high-throughput qPCR analysis in R and Bioconductor" April 14, 2011 as a guide but the example in section 13 is for 48*48 arrays. I tried to modify the …
updated 11.9 years ago • Norm Allaire
CONV F 1816 LOW CONV M 1818 LOW CONV F 1822 LOW CONV M 1826 LOW CONV F 1828 LOW CONV F 1764 NORM CONV F 1770 NORM CONV F 1782 NORM CONV M 1792 NORM CONV M 1802 NORM CONV F 1804 NORM CONV F 1755 HIGH HCHF M 1767 HIGH HCHF F 1777...HCHF F 1783 LOW HCHF M 1785 LOW HCHF M 1807 LOW HCHF F 1821 LOW HCHF M 1827 LOW HCHF F 1761 NORM HCHF F 1763 NORM HCHF F 1769 NORM HCHF M 1789 NOR…
updated 6.9 years ago • sharmila.ahmad
colnames(design) &lt;- c("s1", "s2") #process bg &lt;- backgroundCorrect(agi, method = "normexp") norm &lt;- normalizeBetweenArrays(bg, method = "cyclicloess") avg &lt;- avereps(norm, ID=norm$genes$ProbeName) #fit contmat &lt;- makeContrasts...applies subtraction background correction with limma bg_subtract &lt;- function(x){ return(list(norm = x$norm, …
lt;- info$ID libsizes plot(indiff_count) indiff_norm &lt;- dba.normalize(indiff_count) norm &lt;- dba.normalize(indiff_count, bRetrieve=TRUE) norm normlibs &lt;- cbind(FullLibSize=norm$lib.sizes, NormFacs=norm$norm.factors...NormLibSize=round(norm$lib.sizes/norm$norm.factors)) rownames(normlibs) &lt;- info$ID normlibs #Continue with DiffBind to obtain differenti…
updated 4.6 years ago • Nico
Code: <pre> AF.mydata &lt;- ReadAffy() AF.esetRMA&lt;-rma(AF.mydata) AF.sampletype &lt;- c('Norm','Norm','Norm','Mut','Mut','Mut','Mut',) AF.group &lt;-factor(AF.sampletype) AF.fit &lt;- lmFit(AF.esetRMA,AF.design) AF.contrast.matrix...lt;-makeContrasts(Norm-Mut,levels=AF.design) AF.fit2&lt;- contrasts.fit(AF.fit,AF.contrast.matrix) AF.fit2 &lt;- eBayes…
updated 11.1 years ago • Bade
I do not get best results with cosine distance, which is the usual distance measure I choose. L1 norm, L2 norm, L3 norm all seem to work better, but I am not sure which one is the best and I could not think of a theoretical justification
updated 8.3 years ago • alexanderaivazidis
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updated 19.3 years ago • James Anderson
Hi Gordon, I used to use predFC() to get modified log count-per-million values per sample but now I'm switching to cpm(). I just realized that predFC() doesn't use the normalization factors in the DGEList object when design=NULL, but it does appear to use them when the design is specified (see example below) and there is no argument to specify them, unlike cpm(). Is this a bug or the intended b…
updated 12.4 years ago • Jenny Drnevich
in edgeR are: library(edgeR) dge &lt;- DGEList(counts = counts, group = group ) norm &lt;- calcNormFactors(dge,method="TMM") d &lt;- estimateGLMCommonDisp(norm, design = design) d &lt;- estimateGLMTrendedDisp(d,design...log(counts)[,1], where i is the index of each individual (each row in the count matrix). Then I used norm&am…
updated 11.4 years ago • Zhan Tianyu
3Dlist(maNormMed()),f.scale=3Dlist(maNormMAD()) ) giv= e a different result from using y=3DmaNorm(x,norm=3D=B2median=B2) and z=3DmaNormScale(y,norm=3D=B2globalMAD=B2) serially? Thanks, Sean [[alternative HTML version deleted]] </div
updated 22.0 years ago • Sean Davis
expressions (rows) and the output (norm). *data* GSM276723.CEL GSM276724.CEL GSM276725.CEL GSM276726.CEL norm 0.897000 0.590000 0.683000 0.949000 206427_s_at...5.903681 5.658115 GSM276732.CEL GSM276735.CEL GSM276736.CEL GSM276737.CEL norm 0.43400 0.647000 0.113000 1.000000 206427_s_at 12.80257 5.645002…
updated 16.2 years ago • Eleni Christodoulou
<div class="preformatted">Dear all, 1- In normalizeCtData for norm="geometric.mean" , Can we average over all arrays or should we obrain the geometric mean of all samples? 2- geo.mean.ref= apply...div class="preformatted">Dear all, 1- In normalizeCtData for norm="geometric.mean" , Can we average over all arrays or should we obrain the geometric mean of all samples? 2- geo.mean.ref...bu…
updated 13.8 years ago • Ali Mohammadian
Hi, I have 2 bed files from 2 control samples that have single nucleotide reads over a region. I would like to calculate the average coverage (and standard deviation) between the 2 samples at each base. I have calculated the size factors for each library to normalize the reads before averaging. I have also extended the reads by 100 basepairs to smooth out the coverage. I can easily make bigwigs …
updated 5.1 years ago • Jake
Chromosome #Setup design (from snapCGH guide) stuff$design &lt;- c(-1,-1) #Normalisation within normed &lt;- normalizeWithinArrays(stuff, method="loess") #Get rid of "genes" with no location information normed$genes &lt;- normed...genes[!(is.na(normed$genes$Chr)) &amp; normed$genes$Chr != "",] #ProcessCGH normed2 &lt;- processCGH(normed, method.of.averaging = mean,ID="Prob…
updated 18.9 years ago • Daniel Brewer
y&lt;-dt(x1[1:(n.points/2)],DOF[j]) y&lt;-c(y,rev(y)) y/sum(y)/Norm }) Tmp&lt;-multi_conv(PDF) Tmp = Tmp*(n.points-1)/MaxDiff[i]/2 }else{ warning(paste("Gene set: (index ",i, ") has 0 overlap with eset.",sep="")) Tmp...if(!silent &amp; i%%5==0){cat(".")} Indexes = geneSets[[i]] if(length(Indexes)!=0){ N…
updated 11 months ago • oliverd
<div class="preformatted"> I have a custom Affy array which allows several applications (expression profiling, genotyping, etc...) on a single chip. I want to use RLMM to analyze our genotyping data, but have a couple of questions: 1) Instead of normalizing to the scale of the training set (which I don't have), does it make sense to normalize all arrays to each other using quantile normal…
geo/query/acc.cgi?acc=GSM803742 &nbsp;is it rma wich converts it too log2 like this: &gt;&nbsp;norm &lt;- rma(raw); expr &lt;- exprs(norm); &gt;Pda &lt;- fitPLM(raw, model = PM ~ -1 + probes + samples) Thanks, Anna &nbsp
updated 10.9 years ago • kanacska
preformatted">dear all: i have two questions 1. is the "size factor" from DESeq equally to the "norm factor" in the edgeR 2. i can get the normalized counts by counts(obj,normalized=T) how to get normalized counts from edgeR...can i use the each col of count matrix divided by norm factor -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14…
updated 13.5 years ago • wang peter
FALSE, background=T, library=DBA_LIBSIZE_BACKGROUND, normalize=DBA_NORM_LIB) db_data_spikeinNorm2$norm$DESeq2$lib.sizes [1] 7424321 7030471 8640826 7006223 &gt; db_data_spikeinNorm2$norm$background$binned$totals [1] 7424321...TRUE, background=T, library=DBA_LIBSIZE_BACKGROUND, normalize=DBA_NORM_LIB) db_data_spikeinNorm3$norm$DESeq2$lib.sizes [1] 7747122 7334460 9112179 7386926 db_data_sp…
updated 2.8 years ago • Weisheng
<div class="preformatted">Hello, I'm new to marray, and after reading all of the tutorials and playing around with my data, I find myself in need of a bit of advice. I am attempting to load a batch of GenePix files and conduct a loess normalization on the unflagged spots. I'm having no problem normalizing the data using the approach below, but I am unsure whether the weight matrix is bei…
updated 19.6 years ago • Oliver R. Homann
swirl yy &lt;- maNormMain(x,f.loc=list(maNormMed()),f.scale=list(maNormMAD())) z1 &lt;- maNorm(x, norm="m") z2 &lt;- maNormScale(z1, norm="globalMAD") par(mfrow=c(2,2)) for(i in 1:4) plot(maM(z2)[,i], maM(yy)[,i]) Could you described a little more how
updated 22.0 years ago • Jean Yee Hwa Yang
Hi all, I have a question related to ChIP-seq spike-in normalization as illustrated on the csaw vignette. The idea of calculating a norm factor on the spikes data is great. But as mentionned in the vignette, using the normoffset function on the spike (...) _assume that the library sizes are the same between spike.data and endog.data_ (...). However, in my case, I did two seperate mappings (one…
updated 7.2 years ago • Nicolas Servant
offset=1) boxplot(as.data.frame(Enorm$E), main="Mean intensities - normexp") #Normalisation quantile NormE &lt;- normalizeBetweenArrays(Enorm,method="quantile") boxplot(as.data.frame(NormE$E), main="Normalized intensities") NormE...E &lt;- log2(NormE$E) pData &lt;- data.frame(population = c('mal','mal', 'mal', 'mal','mal','mal','mal','mal','mal','mal','mal','mal','mal','mal','sai n'…
updated 14.4 years ago • bigoun
to get stuck in a loop marrayNorm 1.1.1 &gt; unix.time(experiment1.norm&lt;-maNorm(experiment1, norm="loess")) [1] 803.99 29.73 843.40 0.00 0.00 marrayNorm 1.1.3 (installed with bioconductor 1.2) &gt; unix.time(experiment1.norm...lt;-maNorm(experiment1, norm="loess")) Timing stopped at: 8874.73 19.65 10289.06 0 0 ie I interrupted the process. is there a known problem with …
updated 22.5 years ago • Rob Dunne
value after &gt; normalization?? &gt; Min Normalized : ???? &gt; Max Normalized : ???? &gt; StdErr Norm : ???? &gt; StdDev Norm : ???? &gt; t-test P-value : P-value &gt; Flags [A,M,P] : A - Absent; P - Present ; M - ??? &gt; Raw : ???? &gt; Min Raw : ???? &gt; Max Raw : ???? &gt; StdErr Raw : ???? &a…
updated 20.9 years ago • S Peri
1.1.3 (installed with bioconductor 1.2) &gt; unix.time(experiment1.norm&lt;-maNorm(experiment1, norm="loess")) Timing stopped at: 8874.73 19.65 10289.06 0 0 ie I interrupted the process - but with marrayNorm 1.1.1 reinstalled...marrayNorm 1.1.1 &gt; unix.time(experiment1.norm&lt;-maNorm(experiment1, norm="loess")) [1] 803.99 29.73 843.40 0.00 0.00 is there a known proble…
updated 22.5 years ago • Rob Dunne
or I am doing something wrong? I have tried the following normalizations: 1. normp &lt;-maNorm(raw, norm="p") 2. normg&lt;-maNormScale(normp, norm ="g") In each case the scatter plot yields a slope of .5 rather than 1. Any suggestions would
1000, lc = 0) myTMM myfilt = filtered.data(countsTable, factor = conditions$Cellular\_Type, norm = FALSE, depth = NULL, method = 1, cv.cutoff = 100, cpm = 1, p.adj = "fdr") mynoiseq = noiseqbio(mydata, k = 0.5, norm = "tmm", factor="Cellular\_Type
updated 7.7 years ago • Aurora
Context: I've been doing some in silico research involving large-scale simulations with various DGE packages. I detected an error (detailed below) in my simulations that seemed new to edgeR 4.2.1 and did not occur in earlier versions. The following example might involve some non-sensical data, but I was able to reduce the original, meaningful, large-scale simulation dataset to this 3 by 3 one f…
updated 15 months ago • Hongjian
colnames(design) &lt;- c("s1", "s2") #process bg &lt;- backgroundCorrect(agi, method = "normexp") norm &lt;- normalizeBetweenArrays(bg, method = "cyclicloess") avg &lt;- avereps(norm, ID=norm$genes$ProbeName) #fit contmat &lt;- makeContrasts...bg = bg, desg = desg, norm = norm) processed &lt;- matrix(NA, nrow = …
access the slot 'count'. After fixing that, it runs into: Error in qpHexbin(mnorm, main = "MA-Plot :: Norm") : couldn't find function "hexagons" Error in qpHexbin(mnorm, main = "MA-Plot :: Norm") : couldn't find function "hex.legend" Which I also
updated 20.6 years ago • Rob J Goedman
normalizations in a row with the default. That is to say I have done: ira.norm &lt;- maNorm(ira.raw, norm = "p") ira.x2.norm &lt;- maNorm(ira.norm, norm = "p") The curves flattened considerably. Is there a potenial problem with this procedure
updated 21.9 years ago • Richard Friedman
I would like to take out raw counts from __gene X __from matrix __A__, and use the lib-size and norm-factors from a DGEList-object based on matrix __B__. How do I calculated the normalized expression of gene X? Thanks, &nbsp
updated 7.6 years ago • R
j in 1:(i - 1)) { mm &lt;- subdata[, c(i, j)] rs5 &lt;- rowSums(mm) &gt; 5 norm &lt;- t(t(mm)/colSums(mm)) * gm(colSums(mm)) delta &lt;- optimize(myFun, interval = c(1e-04, 0.99), tol = 1e-06, maximum = TRUE, y = norm[rs5, ], der = 0, doSum
updated 13.2 years ago • Guest User
data analysis, for that I am using a matrix of log Fold change values generated by: <pre> norm &lt;- assay(normTransform(dds)) i &lt;- seq.int(1L,72,by = 2L) # 72 is the total number of samples. norm.fc &lt;- norm[,i]-norm[,i+1]​ write.table
updated 9.3 years ago • g.atla
function 'featureNames' for this call This information is available in the marrayNorm object: &gt; norm at maGnames@maInfo[1:10,] ID Name X22170 22170 DXF68S1E X21642 21642 ABCA2 X22209 22209 LOC56990 X22121 22121 PDZD2 X24284...GGA2 X22739 22739 FLJ14566 I can fix the gene names by doing the following geneNames(monkey) &lt;- norm at maGnames@maInfo$Name…
updated 19.5 years ago • Daniel Brewer
<div class="preformatted">Hello, I'm not sure if this is a known issue, but I have been experiencing unpredictable results with the warpSet function in flowStats (see sessionInfo at end). Essentially, I have a been experimenting with warpSet and have it in a script that runs through the same 5 fcs files as a flowSet each time. About every 2 out of 3 runs I get this error with warpSet: par…
updated 15.6 years ago • Aric Gregson
library(reb) expr &lt;- justRMA() matrix &lt;- assayData(expr)$exprs #Define oncocytoma as norms norms &lt;- 16:30 chr &lt;- buildChromLocation.2("hgu133plus2.db","bands") cset &lt;- reb(matrix,chr,ref=norms,center=TRUE) exprs...lt;- cset[,-norms] exprs[abs(exprs) &lt; 1.96] &lt;- NA banded &lt;- cset2band(exprs,chr,FUN=mean,na.rm=TRUE) h.cyto &lt;- bui…
dgelist &lt;- DGEList(matrix) ##the matrix with gene names as row names and counts in columns norm-mat &lt;- calcNormFactors(dgelist, method = "TMM") norm-mat &lt;- cpm(norm-mat, log = TRUE) For DESeq2: DESeq2 requires integers as input
updated 4.2 years ago • BioNovice247
1 dis 2 2A7_Hex_07Jul_09.CEL 1 dis 3 2A8_Hex_07Jul_09.CEL 1 dis 4 2A9_Hex_07Jul_09.CEL 1 norm 5 2AA_Hex_07Jul_09.CEL 1 norm 6 2AB_Hex_07Jul_09.CEL 1 norm </div
updated 14.1 years ago • Fabrice Tourre
installed with bioconductor 1.2) &gt; &gt; unix.time(experiment1.norm&lt;-maNorm(experiment1, norm="loess")) &gt;Timing stopped at: 15358.18 19.85 20734.47 0.00 0.00 &gt; &gt;ie I interrupted the process - &gt;but with marrayNorm...reinstalled &gt; &gt; marrayNorm 1.1.1 &gt; &gt; unix.time(experiment1.norm&lt;-maNorm(experiment1, norm="…
updated 22.3 years ago • Rob Dunne
Read 23148733 records Read 21898540 records [0% done] Starting chr:80000-1e+05:Error in var(tr$"+"$norm[x[1]:x[2]]) :&nbsp; &nbsp; error in evaluating the argument 'x' in selecting a method for function 'var': Error in tr$"+"$norm[x[1]:x[2]] :&nbsp; &nbsp
updated 10.4 years ago • Reed
FALSE, quantile=0.9, groups =files$Group, verbose=TRUE) s.norm &lt;- normalizeCtData(raw.cat, norm="scale.rank") exprs(s.norm) write.table(exprs(s.norm),file="Ct norm scaling.txt") g.norm &lt;- 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 expression value fil…
updated 12.3 years ago • Guest User
FALSE, quantile=0.9, groups =files$Group, verbose=TRUE) s.norm &lt;- normalizeCtData(raw.cat, norm="scale.rank") exprs(s.norm) write.table(exprs(s.norm),file="Ct norm scaling.txt") g.norm &lt;- normalizeCtData(raw.cat, norm...geometric.mean") exprs(g.norm) write.table(exprs(g.norm),file="Ct norm media geometrica.txt") Now if we look at the content of the two expression value fil…
updated 12.3 years ago • Guest User
metagenomeSeq's function "aggTax" to aggregate:</span> &nbsp; &nbsp; AggObj = aggTax(MRcounts(obj, norm=TRUE, log=FALSE),norm=TRUE, log=FALSE, lvl = Class, out = "MRexperiment") As you can see, I am using the normalized counts for aggregation
updated 10.9 years ago • noelle.noyes
handy later on. The parts that should interest you most are the highcut and lowcut options. The normed and rawout options are not used that often. I last ran this code under R 2.6.1, so I am not sure if it will work without a...0, method = "loess", lowcut=0, highcut=195000, bw = 0.1, rawout=FALSE,normed=FALSE, SpecNames = list.files(fldr, patter…
updated 16.1 years ago • Davis, Wade
1 print tip is present), but it did end up making the code crash. This can be fixed by specifying norm='l' (if loess normalization is wanted) in the agQuality. I think that should be the default in agQuality and change (in agQuality...defs &lt;- list(norm = "p") to defs &lt;- list(norm = "l") As a note, the diagnostic spatial images being produced are not correct either. It prod…
the group representing each individual chipseq run, and then creating a design matrix to calculate norm factors, estimate dispersion, and perform glmQLFtests (following p.8 of the edgeR manual
updated 7.9 years ago • james.dalgleish
address 0x110660000, cause 'memory not mapped' Traceback: 1: .Call("bayespeak", as.integer(tr$"+"$norm[659981:720020]), as.integer(tr$"-"$norm[659981:720020]), as.integer(w$norm[659981:720020]), as.double(w$norm[659981:720020]), as.integer...max(w$norm[659981:720020])), as.integer(60000), as.character(ch), start = as.integer(83925925), end = as.integer(89929925), as.integer(bin.size
updated 15.6 years ago • Tim Rayner
results = res, sep = sep, file = paste(c(x[[1]]$bg, x[[1]]$norm, "lmfit.csv"), collapse = "")) write.fit(fit2, results = res, sep = sep, file = paste(c(x[[1]]$bg, x[[1]]$norm, "be.csv"), collapse = "")) where x[[1]]$avg is the corrected
updated 12.8 years ago • Cornish, Joseph NIH/NIAID [F]
254 61 80 79 876 571218 131 42 61 47 246 &gt; Norm&lt;-normalize.quantiles(BG) &gt; dim(Norm) [1] 473162 15 &gt; Norm[1:10,1:5] [,1] [,2] [,3] [,4] [,5] [1,] 128.4667 143.40000 114.06667 332.7333 230.0000...195.80000 482.5333 602.5667 [10,] 125.7333 89.73333 131.33333 103.0667 187.9333 &…
updated 17.5 years ago • Ann Hess
FALSE, quantile=0.9, groups =files$Group, verbose=TRUE) s.norm &lt;- normalizeCtData(raw.cat, norm="scale.rank") exprs(s.norm) write.table(exprs(s.norm),file="Ct norm scaling.txt") g.norm &lt;- 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 expression value files, it …
updated 12.4 years ago • Guest User
access the slot 'count'. After fixing that, it runs into: Error in qpHexbin(mnorm, main = "MA-Plot :: Norm") : couldn't find function "hexagons" Error in qpHexbin(mnorm, main = "MA-Plot :: Norm") : couldn't find function "hex.legend" Which I also
updated 20.6 years ago • Paquet, Agnes
of memory. apt-cel-extract -o out.txt [-c chip.clf -p chip.pgf] [-d chip.cdf] \ --probeset-ids=norm-exon.txt --probeset-ids=norm-intron.txt \ --probe-ids=antigenomic.bgp *.cel Hope it helps Raffaele shirley zhang wrote: &gt
updated 17.8 years ago • raffaele calogero
work for my data set and I am getting the following error message: &gt; dat.Norm = maNorm(dat.RAW, norm="p") Error in simpleLoess(y, x, w, span, degree, parametric, drop.square, normalize, : invalid `x' Is there any way to use maNorm() successfully
updated 22.0 years ago • Mahbub Latif
against a single normalization control. Below is the code and the error. <pre> &gt; NORM &lt;- "hsa-miR-30a-5p" &gt; idx &lt;- which( rownames( Counts.deseq )==NORM ) &gt; Counts.deseq.cnorm &lt;- estimateSizeFactors( Counts.deseq
updated 10.9 years ago • Johannes Rainer
nbsp; Here is my code: <pre> eset57338 &lt;- (getDataset("GSE57338", "GPL11532",format = "CURESET", norm = "SCAN", features = "GENE")) eset42955 &lt;- (getDataset("GSE42955", "GPL6244", format = "CURESET",norm = "SCAN", features = "GENE")) thelist &lt;- list
updated 10.5 years ago • Vani
Hi! I have some questions in eliminating efficiency after reading the csaw user's guide. In the examples of the user's guide, two of them filter windows and then use TMM for normalization to eliminate composition biaes. However, in [5.3 Eliminating efficiency biases](http://bioconductor.org/books/3.15/csawBook/chap-norm.html#sec:eff-norm), windows are also filtered first and then applied to TMM…
updated 2.9 years ago • sashu
230 results • Page 1 of 4
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