User: Claire Wilson
Claire Wilson • 280
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Posts by Claire Wilson
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... Or alternatively you can use rowSums (assuming x contains your matrix
of
PMA calls):
calls.sum <- rowSums(x=="P")
keep <- names(calls.sum[calls.sum>=2])
It's a little faster!
claire
--
Claire Wilson
Bioinformatics Group
Paterson Institute for Cancer Research
Christie Hospital NHS Trust
W ...
written 14.2 years ago by
Claire Wilson • 280
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Answer:
A: filtering for present calls
... Hi Josh,
Not sure whether anyone has responded to your mail yet, but I think an
easier way to do this would be to load your data in, normalise it then
calculate detection calls (present/absent calls) and then use these to
filter only out those probesets called present..
library(simpleaffy)
library ...
written 14.4 years ago by
Claire Wilson • 280
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... Hi Christian,
This error arises because simpleaffy doesn't know what the alpha1 and
alpha2 values are for the Hu6800 chips and you need to supply them
with
the call to detection.p.val
pv17 <- detection.p.val(M17, alpha1=X,alpha2=Y)
Hope this helps
Claire
> -----Original Message-----
> ...
written 14.7 years ago by
Claire Wilson • 280
• updated
14.7 years ago by
Christian.Stratowa@vie.boehringer-ingelheim.com • 270
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... Dear all,
We found similar things when we looked at the standard and small
sample
(amplification) protocols from Affymetrix (Wilson et al 2004,
Biotechniques. 2004 Mar;36(3):498-506). Whilst raw expression levels
from unamplified and amplified arrays were not directly comparable,
fold-changes were ...
written 14.8 years ago by
Claire Wilson • 280
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Answer:
A: mas5call select genes
... Hi Katleen,
This is the function I use on a matrix of Affymetrix Absent/Present
calls (rows are probesets, columns are chips)
number.pres <- function(x) {
x[x=="P"] <- 1;
x[x!=1] <- 0;
return(apply(x,1,function(a) { sum(as.integer(a))}))
}
# Calculate present/a ...
written 14.9 years ago by
Claire Wilson • 280
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...
> Dear Users,
>
> I am following the example on Lab 5: Cluster analysis (June
> 2003) with
> my own data.
>
> I have filtered my expression set as shown on the example and I get
> the following
>
> > sub <- genefilter(X,ffun)
> > sum(sub)
> [1] 1124
> ...
written 15.1 years ago by
Claire Wilson • 280
• updated
15.1 years ago by
rgentleman • 5.5k
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Answer:
A: heatmap genenames
...
Hello,
Many thanks for your reply, I have tried repeating the clustering done
by heatmap using hclust to obtain the row order as follows:
d <- dist(mydata)
hc.d <- hclust(d)
gene.order <- hc.d$order
and compared the order to what I see on a heatmap when I do
heatmap(mydata)
However, i ...
written 15.1 years ago by
Claire Wilson • 280
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... Dear all,
I have been using the heatmap function to visualise my data and would
like to obtain a list of my genes in the same order that they appear
in
the heatmap. I have looked through the mail archives and tried just
creating a dendogram and using order.dendogram but have so far been
unsuccessfu ...
written 15.1 years ago by
Claire Wilson • 280
• updated
15.1 years ago by
Francois Pepin • 1.3k
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... The simpleaffy package has a function screenpng that will allow you to
save any images as .png files
hope this helps
claire
> -----Original Message-----
> From: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of SAURIN
> Sent: 20 June ...
written 15.5 years ago by
Claire Wilson • 280
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... Dear all,
I have been working through the factDesign vignette and it appears
that
the probeset identifiers have been lost from the expression set and
also
that the expression calls appear to not be in log2 form as indicated
in
the vignette(code shown below)...thanks for any help, claire
> librar ...
written 15.6 years ago by
Claire Wilson • 280
• updated
15.6 years ago by
Denise Scholtens • 40
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