User: Ron Ophir

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Ron Ophir270
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Posts by Ron Ophir

<prev • 27 results • page 1 of 3 • next >
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heatmap_2
... Hi, One of the features of heatmap is to set Colv or Rowv to NA if I don't wont to perform clustering on columns or rows respectively. This option does not exist in heatmap_2. Is there another way to show columns or rows cluster solely? Thanks, Ron ...
clustering written 13.2 years ago by Ron Ophir270 • updated 13.2 years ago by Marc Saric70
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[limma] 3-Way Factorial design
... Dear All, As it described in Limma User's Guide chapter 8.7 there are more than one approach to create the design and contrst matrices. I would like to focus in this question on the first example where in the design matrix one creates all possible combinations between the factors. Thus for target f ...
limma written 13.4 years ago by Ron Ophir270
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promotor tilingArray
... Dear list, Does any one know which packge deals with chromatine immuno-percipitation (ChiP) on human promotor chip. We have Cel files files which can be inserted into AffyBatch object. However the mapping is done by BPMAP (Binary Probe MAPping file) rather then CDF file. Thanks, Ron ...
cdf probe written 13.4 years ago by Ron Ophir270
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[heatmap] different distance functions for columns and for rows
... I see. I missed it. You mean something like this x<-matrix(rnorm(1000,10,2),100,100) hc<-as.dendrogram(hclust(dist(x,method="euclidean"))) hr<-as.dendrogram(hclust(as.dist(cor(x,method="pearson")))) x11();hv <- heatmap(x,Rowv=hr,Colv=hc) Thanks, Ron >>> Sean Davis 30/05/200 ...
clustering written 13.5 years ago by Ron Ophir270
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[heatmap] different distance functions for columns and for rows
... I would like to run clustering on columns (samples) and rows (genes) and get a plot similar to the output of heatmap(). However I would like to apply euclidean distance to samples and pearson distance to genes. Is it possible to do it with heatmap(). If not, is there other function that can do it? ...
clustering written 13.5 years ago by Ron Ophir270 • updated 13.5 years ago by Sean Davis21k
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Another question about dye swap
... Thanks Gordon, I mixed up as a result of what I read in "Introductory statistic with R" where there is an example of (section 10.2) x<-runif(20) y<-2*x+rnorm(20,0,0.3) summary(lm(y~x)) gives insignificant intercept so there is a suggestion to run summary(lm(y~x-1)) but when I run once model.m ...
go limma written 13.8 years ago by Ron Ophir270 • updated 13.8 years ago by Giorgi, Elena30
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Another question about dye swap
... Hi, >From limma user guide section 8.1.2 Simple comparisons -> Dye swaps it is clear that for the following experimental design: FileName Cy3 Cy5 File1 wt mu File2 mu wt File3 wt mu File4 mu wt *(four replicates of two groups (wt , mu) of which two replicates in eac ...
go limma written 13.8 years ago by Ron Ophir270
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Answer: A: RMA normalization when using subsets of samples
... Dear all, I think that D.R. Godstein has tried to answer Sylvia's question in http://ludwig-sun2.unil.ch/~darlene/ms/prRMA.pdf Ron >>> 02/15/06 11:55 AM >>> Dear Martin, We have run up to 550 chips achieving a reasonable processing time -- not more than an hour or so. The pr ...
written 13.8 years ago by Ron Ophir270
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Removing Batch effect with Limma
... Hi, I have the following MA experiment running on Affymetrix technology. It includes 4 condition and 3 time points for each condition as follow: FileName Targets Time Treatment Batch F21.CEL I18 18 I 3 F22.CEL I18 18 I 3 F25.CEL N18 18 N 3 ...
written 13.9 years ago by Ron Ophir270
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[LIMMA] change in normexp function between limma 2.2.0 to limma 2.4.4
... Hi, We have a microarray experiment of cDNA of 36 spotted arrays, reference design. Two persons run the analysis with same code and the same data for education purposes. One loaded limma package version >sessionInfo() R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "meth ...
microarray limma written 14.0 years ago by Ron Ophir270

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