User: Hans-Ulrich Klein

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330
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Posts by Hans-Ulrich Klein

<prev • 32 results • page 3 of 4 • next >
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vsn2 and print-tips
... Dear all, I use the vsn2 method to normalize single-colour arrays with 48 print-tips (25*26 oligos per print-tip). After normalization, the intensities of the 48 print-tips are in different ranges. The grid of the print-tips can be seen clearly on false color representations of the arrays' spatial ...
normalization written 11.8 years ago by Hans-Ulrich Klein330 • updated 11.8 years ago by Wolfgang Huber13k
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contrasts in limma and missing values
... Dear List, I have a question concerning missing values in limma. Consider the following short example: M = rbind(c(10,9,5,4,5,12,13,7,8),c(10,9,5,4,5,12,13,7,8)) w = rbind(c(1,1,1,1,1,1,1,1,1),c(1,1,1,1,1,0,0,0,0)) class = factor(c(1,1,2,2,2,1,1,2,2)) lab = factor(c(1,1,1,1,1,2,2,2,2)) design = ...
limma written 12.1 years ago by Hans-Ulrich Klein330
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batch effects and VSN
... Hello List, I am analyzing some arrays with strong "batch effects". The source of the variation is unknown. The biologists and I found out that some of the systematic variation is related to some processing steps in the laboratory (ChIP-experiment). My first general question is how do you deal wit ...
normalization regression vsn limma oligo written 12.2 years ago by Hans-Ulrich Klein330 • updated 12.2 years ago by Wolfgang Huber13k
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globaltest - multinomial model
... Hi List, I get a warning message whenever I use the function globaltest with a multinomial model. Below is a code example taken from the vignette leading to the warning message: Warning message: $ operator not defined for this S4 class, returning NULL in: fit$iter Should I be concerned about the w ...
survival affy vsn limma globaltest affyio written 12.3 years ago by Hans-Ulrich Klein330 • updated 12.3 years ago by Goeman, J.J. MSTAT150
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Affymetrix annotation package
... Dear list, I wonder about the annotation of some probesets on Affymetrix chips. E.g.: > library("hgu95av2") > get("1726_at", env=hgu95av2ACCNUM) [1] "HG919-HT919" Is "HG919-HT919" really an accession number? I do not get any hits at NCBI's GenBank. NetAffx gives the same identifier for that ...
annotation written 12.4 years ago by Hans-Ulrich Klein330 • updated 12.4 years ago by John Zhang2.9k
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Answer: A: VSN 2.2
... Hi all, I noticed that the function "vsn2" is much slower than the function "vsn". Probably it is not a general problem, but at least for my dataset the difference in computation time is remarkable: > vsnResG <- vsn(RG$G[subSet,1:5], strata=RG$genes$Block[subSet]); vsn: 25727 x 5 matrix (4 ...
written 12.6 years ago by Hans-Ulrich Klein330
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Comment: C: VSN 2.2
... Dear Wolfgang, thank you very much for your fast and detailed response! Wolfgang Huber wrote: > [...] > Hope this helps, please let me know, > How do the scatterplots of old versus new glog-ratios look like? I plotted old versus new glog-intensities instead of ratios (only the green chan ...
written 12.6 years ago by Hans-Ulrich Klein330
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VSN 2.2
... Dear all, I want to normalize a matrix of gene expression values G using VSN. With VSN 1.x I did > vsnRes <- vsn(G) > Gvsn_old <- exprs(vsnRes) / log(2) This still works with vsn 2.2 (besides deprecated warnings) and computes exactly the same values as the older version of vsn does. ...
normalization vsn written 12.6 years ago by Hans-Ulrich Klein330 • updated 12.6 years ago by Wolfgang Huber13k
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GlobalAncova
... Dear List, I have a couple of covariates in conjunction with my gene expression values. I want to know, whether some of the covariates have an influence on the expression values. The GlobalAncova package seems to be able to answer this question. "data" is a matrix (genes x samples) with gene expre ...
globalancova written 12.7 years ago by Hans-Ulrich Klein330
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saturated spots
... Dear all, I currently analyse some selfmade oligo chips. The green channel contains the results of a ChIP-experiment. The red one contains genomic DNA. I read in the data and did some quality plots using limma. Unfortunatly, most arrays show strong saturation effects. Some plots for interested rea ...
limma oligo written 12.9 years ago by Hans-Ulrich Klein330 • updated 12.9 years ago by J.delasHeras@ed.ac.uk1.9k

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Popular Question 5.2 years ago, created a question with more than 1,000 views. For Affymetrix Human Gene 1.0 ST Array

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