User: Tan, MinHan

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Tan, MinHan180
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Posts by Tan, MinHan

<prev • 18 results • page 1 of 2 • next >
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Answer: A: hclust and (Eisen+ de Hoon) cluster3 program
... 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 14.9 years ago by Tan, MinHan180
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Application of PAMR from Affy to spot data
... 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 ...
affy pamr written 15.1 years ago by Tan, MinHan180 • updated 15.1 years ago by rgentleman5.5k
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Citing R / Bioconductor
... 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 ...
annotation affy written 15.3 years ago by Tan, MinHan180
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Hierarchical clustering and shrinking centroids...
... 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 ...
classification clustering pamr written 15.4 years ago by Tan, MinHan180 • updated 15.4 years ago by Stephen Henderson1.0k
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Answer: A: memory usage ReadAffy() and probe level information
... 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 15.5 years ago by Tan, MinHan180
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Bug with R 1.9.0 beta (3/23) and PAMR?
... 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 ...
pamr written 15.6 years ago by Tan, MinHan180 • updated 15.6 years ago by Liaw, Andy360
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Filtering Affymetrix data towards class discovery
... 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 ...
affy written 15.6 years ago by Tan, MinHan180
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Question about excluding Affymetrix spike controls from normalization
... 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 ...
normalization bacillus subtilis convert written 15.7 years ago by Tan, MinHan180
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Combine function in matchprobes
... 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 ...
cdf matchprobes written 15.8 years ago by Tan, MinHan180 • updated 15.8 years ago by rgentleman5.5k
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Advice re: HGU133A and HGU133 Plus2.0
... 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 ...
hgu133a probe written 15.8 years ago by Tan, MinHan180

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Popular Question 14.9 years ago, created a question with more than 1,000 views. For Citing R / Bioconductor

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