User: Hinnerk Boriss
Hinnerk Boriss • 220
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Posts by Hinnerk Boriss
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Answer:
A: normalization for custom chip
... Dear Shibing,
I do not recommend using house keeping genes for normalization. In
several
experiments they turn out being differentially expressed. A better
approach
would be to use a normalization method that searches for an invariant
set of
genes in the sample. "VSN" and Li & Wong's "invariant ...
written 15.1 years ago by
Hinnerk Boriss • 220
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... Hi,
I tried to install the new version 1.4, however, noticed that neither
the default (getBioC() ) nor explicitly calling getBioC("cdna") would
install the vsn library. That is confusing as the installation
instructions say that this should work. How can that be fixed?
Best regards,
Hinnerk ...
written 15.5 years ago by
Hinnerk Boriss • 220
• updated
15.5 years ago by
Johannes Freudenberg • 30
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... Hi Kevin,
did you do in vitro amplification of your samples to increase the cRNA
available for hybridization? This is a common source of the problem
you
are describing. There are no mathematical methods for retrofixing this
problem.
> Q1: Do you have any arguments against the RMA(after)-RMA(befo ...
written 16.0 years ago by
Hinnerk Boriss • 220
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... Hi there!
Has anyone build the annotation package for Affymetrix drosgenome1
chip?
If so, would you share? Many thanks in advance.
Cheers,
Hinnerk ...
written 16.0 years ago by
Hinnerk Boriss • 220
• updated
16.0 years ago by
John Zhang • 2.9k
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Comment:
C: Advice for analyzing Affy data
... Hi!
the Tuckey bigweight summary stat method (mas) does no data
transformation when raw values are supplied in the AffyBatch object,
however, it magically transforms the data when they are log or arcsinh
transformed. What transformation is used? Where could I find out
myself?
And is there a why (op ...
written 16.2 years ago by
Hinnerk Boriss • 220
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Comment:
C: se.exprs
... Hi,
I've been experimenting with the heatmap function of the mva library
and
am not happy with the ordering I get. Does anyone have a good
suggestion? Or could you point me to a documentation of Jonathan
Eisen's
ordering algorithm?
Many thanks in advance,
Hinnerk ...
written 16.4 years ago by
Hinnerk Boriss • 220
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... > > for teaching purposes I would like to cut down the number
> of genes in
> > affybatch objects so that students won't have to wait that long
for
> > their computations. Unfortunately, I cannot figure out how
> to do that.
> > Any hints? Thanks!
>
> Cutting down ...
written 16.5 years ago by
Hinnerk Boriss • 220
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...
> i'd like to add there is a simple way to remove genes. its
> not the best
> way but its simple and itll do the trick:
> say ab is your affybatch and hgu95acdf is your cdf before
> your class type:
>
> 1) library(hgu95acdf) #probably already loaded
> 2) takeout <- ls(hgu ...
written 16.6 years ago by
Hinnerk Boriss • 220
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... Hi there,
for teaching purposes I would like to cut down the number of genes in
affybatch objects so that students won't have to wait that long for
their computations. Unfortunately, I cannot figure out how to do that.
Any hints? Thanks!
Yours dreaming of good old plob objects,
Hinnerk ...
written 16.6 years ago by
Hinnerk Boriss • 220
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... Hi!
What does the p-value of the RNA degradation test actually say and
where
do things begin to become critical?
For instance, I have data here where the p-values are rather low
(hgu133A chips) and in fact the slopes are positive!
What is the appropriate interpretation? No RNA degradation? Somethin ...
written 16.7 years ago by
Hinnerk Boriss • 220
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