User: Francois Collin
Francois Collin • 130
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Posts by Francois Collin
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... who is xlsolutions-corp???
--- Sue Turner wrote:
> XLSolutions Corporation (www.xlsolutions-corp.com)
> is proud to announce:
>
> (1) Introduction to R/S+ programming: Microarrays
> Analysis and Bioconductor
>
> *** San Francisco / July 17-18,
> 2006 ** ...
written 13.4 years ago by
Francois Collin • 130
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... Hello Ren,
Being puzzled in this case is a good thing as there
are no hard and fast rules as to which outlier chips
should be excluded from an analysis. In a sense, the
answer really depends on the analysis in question.
One way to answer the question of which chips should
be excluded, or treated di ...
written 13.7 years ago by
Francois Collin • 130
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... Yes, there is a way to avoid all of the overhead in
lm(). As you are fitting the same model to the data
for all genes, you should only have to get the qr
decomposition of your design matrix once. Here are
some ideas for code - with someting like this you
should get the same results that you would ...
written 15.5 years ago by
Francois Collin • 130
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Comment:
C: unbalanced factorial design
... Running lme on a single probe set takes about 20
minutes computing time on my PC. I'm running R on
windows, which I know can run into memory management
problems, but this problem appears to be completely
cpu bound.
The model that I'm fitting has repeated measures, 6
Visits per Subject, for 20 Subj ...
written 15.6 years ago by
Francois Collin • 130
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... Paul,
The weights are derived from the model fit residuals -
they are transformations of the residuals standardized
by the model fit residual variance (fit here being
probe set specific). Weights will be 1.0 if the
residuals are small compared to the residual variance,
and then decrease toward zero ...
written 15.7 years ago by
Francois Collin • 130
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Answer:
A: iterative gcrma on 92 slides?
... Having to analyze large sets of chips on a PC equipped with little
memory, I had to deal with this issue all the time. Getting rma or
gcrma expression summaries is typcally viewed as a three step process:
background correction, normalization and model fitting. The latter
step, can be further divi ...
written 15.7 years ago by
Francois Collin • 130
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... Dear list:
I know this has been discussed before, but I can't open the link to
the Bioconductor Archives.
My question is regarding the key system requirements to be able to
"comfortably" analyze Affy cel files. The bottleneck on my machine
(more like a dead end) is trying to run bg.adjust.gcrma(). ...
written 15.8 years ago by
Francois Collin • 130
• updated
15.8 years ago by
James W. MacDonald ♦ 51k
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... Dear list:
I know this has been discussed before, but I can't open the link to
the Bioconductor Archives.
My question is regarding the key system requirements to be able to
"comfortably" analyze Affy cel files. The bottleneck on my machine
(more like a dead end) is trying to run bg.adjust.gcrma(). ...
written 15.8 years ago by
Francois Collin • 130
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Comment:
C: RNA digestion plots
... We should keep in mind that systematic differences detected among
probe intensities within a probe sets are tiny in comparison to the
typical variation in intensity observed among probes within a probe
set. Systematic differences are detectable because we are summarizing
probe intensities by locati ...
written 15.9 years ago by
Francois Collin • 130
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... Thanks for the referecne to our work, Wolfgang.
Hope it isn't considered spamming if I put a link to a poster
presentation:
http://www.affymetrix.com/corporate/events/seminar/microarray_workshop
.affx
I concur with Wolfgang that residuals from fits provide great quality
assessment opportunities. ...
written 16.0 years ago by
Francois Collin • 130
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