User: Tan, MinHan
Tan, MinHan • 180
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Posts by Tan, MinHan
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... Did you use a correlation distance metric for hclust?
AFAIK, that's what the Eisen software uses. I think the default
distance
metric for hclust is Euclidean?
Could be wrong, but it's worth a try.
Min-Han Tan
-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch
[mailto:biocon ...
written 14.7 years ago by
Tan, MinHan • 180
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... Good morning,
Sorry for the trouble.
I am trying to apply a pamr gene classifier obtained from Affymetrix
data onto spot cDNA array data. For the Affy data, we have tumors , as
well as several normals. The spot cDNA data is tumor against normal.
I was hoping that I could get the small gene classi ...
written 14.9 years ago by
Tan, MinHan • 180
• updated
14.9 years ago by
rgentleman • 5.5k
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... Good evening,
Just to confirm - is there any change to citing R and Bioconductor?
Citation() does not seem to have been changed?
The last message on this was 1 1/4 year ago - attached below.
Everything is moving so quickly all the time ...!
Thanks.
Min-han
Vincent Carey 525-2265 stvjc at cha ...
written 15.1 years ago by
Tan, MinHan • 180
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... Dear list members,
I have been unable to resolve this conceptual problem.
I performed hierarchical clustering on a filtered sample (cv=0.04, at
least 2 samples > level of log 9) of 80 tumor samples, and obtained
several groups. Some of these clusters were definitely more stable
than
others. Sub ...
written 15.2 years ago by
Tan, MinHan • 180
• updated
15.2 years ago by
Stephen Henderson • 1.0k
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... The limit for justRMA that I have encountered is approximately 110-120
HGU133 Plus 2.0 CEL files, with 2 GB RAM, R 1.9.0 beta running on
Windows. I do not encounter a memory error directly - the R GUI
application just gracefully folds up and reminds me to send an error
report to Bill Gates. Anyway, ...
written 15.4 years ago by
Tan, MinHan • 180
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... Hi,
I hope this is the right place for this bug report:
I am running R.1.9.0 beta (3/23) and PAMR 1.12.1 [most updated
version]
on a Win XP machine.
khan.data <- pamr.from.excel("summary-filter.txt", 75,
sample.labels=TRUE)
pamr.menu(khan.data)
I was running pamr.menu and ran into this error ...
written 15.4 years ago by
Tan, MinHan • 180
• updated
15.4 years ago by
Liaw, Andy • 360
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... Good afternoon,
I have a question on an optimal strategy for filtering of Affymetrix
data (human tumor tissue) geared towards a purpose of class discovery.
(This does not seem to have been directly addressed in the archive).
Since we are not correlating with any clinical outcomes or markers, I
wou ...
written 15.4 years ago by
Tan, MinHan • 180
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... Good evening,
Apologies for the long genelist that follows the text.
I have a question about data analysis - I am hoping to exclude the
bacterial spike in control results from rma normalization (or change
all
corresponding gene values to the same result). (I have included the
list
below) The probl ...
written 15.5 years ago by
Tan, MinHan • 180
0
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... Hi,
I tried combining 2 Affybatches (HGU133A and HGU133Plus 2.0) using
combine in matchprobes, but ran into the following problems.
I used both R 1.9.0 and R 1.8.1 with the latest downloads from
Bioconductor.
> merged.data <- combine(list(DataHGU133A,DataHGU133P),
c("hgu133acdf",
"hgu133plu ...
written 15.6 years ago by
Tan, MinHan • 180
• updated
15.6 years ago by
rgentleman • 5.5k
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... Hello all,
We have a group of array CEL files - half of which are HGU133A and the
other half HGU133 Plus 2.0.
Unfortunately, I need to compare the similar probe sets across the 2
types of chips. I can read the CEL files into different AffyBatches,
but
as they are of different sizes, I am unable to ...
written 15.6 years ago by
Tan, MinHan • 180
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