## User: Hans-Ulrich Klein

Reputation:
330
Status:
Trusted
Location:
United States
Last seen:
5 years, 2 months ago
Joined:
13 years ago
Email:
h******@uni-muenster.de

#### Posts by Hans-Ulrich Klein

<prev • 32 results • page 3 of 4 • next >
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... 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 ...
written 11.8 years ago by Hans-Ulrich Klein330 • updated 11.8 years ago by Wolfgang Huber13k
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... 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 = ...
written 12.1 years ago by Hans-Ulrich Klein330
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... 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 ...
written 12.2 years ago by Hans-Ulrich Klein330 • updated 12.2 years ago by Wolfgang Huber13k
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... 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 ...
written 12.3 years ago by Hans-Ulrich Klein330 • updated 12.3 years ago by Goeman, J.J. MSTAT150
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... 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 ...
written 12.4 years ago by Hans-Ulrich Klein330 • updated 12.4 years ago by John Zhang2.9k
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... 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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... 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. ...
written 12.6 years ago by Hans-Ulrich Klein330 • updated 12.6 years ago by Wolfgang Huber13k
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... 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 ...
written 12.7 years ago by Hans-Ulrich Klein330
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... 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 ...
written 12.9 years ago by Hans-Ulrich Klein330 • updated 12.9 years ago by J.delasHeras@ed.ac.uk1.9k

#### Latest awards to Hans-Ulrich Klein

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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