User: Stefan Thomsen

Reputation:
50
Status:
New User
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Last seen:
11 years, 6 months ago
Joined:
11 years, 8 months ago
Email:
s****@cam.ac.uk

Posts by Stefan Thomsen

<prev • 5 results • page 1 of 1 • next >
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pairs(): different ylim , xlim for upper.panel and lower.panel?
... Dear all, I am trying to create pairs plots with two different panel functions creating MvA and XY scatterplots, respectively. In this context I ran into two problems: 1)I did not manage to assign separate xlim, ylim values to both functions. This is what I tried: panel.mva = function (x, y, . ...
assign written 11.5 years ago by Stefan Thomsen50 • updated 11.5 years ago by Wolfgang Huber13k
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VSN: narrowing down probe sets for parameter estimation
... Dear all, I am working on an Affymetrix time series data set with high percentages (30-40%) and mostly downregulated differentials. In a previous discussion regarding the question of a suitable normalization strategy for such data sets Wolfgang Huber highly recommended to "narrow down the probes f ...
microarray probe vsn written 11.7 years ago by Stefan Thomsen50 • updated 11.7 years ago by Wolfgang Huber13k
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VSN, RMA, dCHIP, etc....
... Dear all, currently evaluating the performance of different normalization strategies to an Affymetrix data set, I have some semi-technical, semi- philosophical questions. Given (i) the jungle of possible normalization strategies implemented in R and other platforms, (ii) the fact that most authors ...
normalization written 11.7 years ago by Stefan Thomsen50 • updated 11.6 years ago by Wolfgang Huber13k
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AffyExpress: AffyQA incompatible with simpleaffy 2.14.04?
... Dear all, previously, AffyQA in AffyExpress could not return certain plots on my data as my Drosophila Genome 2.0 chips were not defined in simpleaffy. The newly released simpleaffy version 2.14.04 allows now easy manual chip definition. However, if I run now AffyQA() after calling library(simplea ...
cdf simpleaffy affyexpress written 11.7 years ago by Stefan Thomsen50
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simpleaffy 2.14.02, setQCEnvironment
... Dear all, I am trying to perform some simpleaffy analyses on Drosophila Genome 2.0 genechips. Following the instructions of the simpleaffy 2.14.02 vignette I set up the following .qcdef file: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at ...
cdf simpleaffy assign written 11.7 years ago by Stefan Thomsen50 • updated 11.7 years ago by Crispin Miller1.1k

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