User: pingzhao Hu

gravatar for pingzhao Hu
pingzhao Hu210
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11 years, 6 months ago
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p**@sickkids.ca

Posts by pingzhao Hu

<prev • 21 results • page 1 of 3 • next >
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Merging microarray datasets
... Kathy, To answer your questions, you may need to know which stages you are trying to integrate your data sets. Roughly speaking, data sets can be integrated at three stages: Say you have two data sets A (affy) and B (cDNA) (1) early stage: first normalize data sets A and B, separately; then someho ...
written 11.6 years ago by pingzhao Hu210
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Answer: A: Call for comments on analyzing aCGH data with huge number of probes on a single
... Sean, Thanks,This is really helpful! I just test the chromosome with 3.5M probes in a single sample, it took less than 20 minutes to get the job done. Dr. Shannon, I also very thank for your useful comments! Have a great weekend. Pingzhao At 12:35 PM 4/4/2008, Sean Davis wrote: >On Fri, Apr ...
written 11.6 years ago by pingzhao Hu210
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Call for comments on analyzing aCGH data with huge number of probes on a single chromosome
... Sean, Thanks! The gold is to identify copy number variation from normal human samples. I have tried CBS, cghFLasso (http://biostatistics.oxfordjournals.org/cgi/content/abstract/kxm013v1 ) our own method (http://biostatistics.oxfordjournals.org/cgi/content/abstract/kxl035v1 ), etc methods. Pingzhao ...
acgh written 11.6 years ago by pingzhao Hu210
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Call for comments on analyzing aCGH data with huge number of probes on a single chromosome
... Hi All, I have a question about analyzing aCGH data with huge number of probes on a single chromosome. We have a set of customized NimbleGen aCGH human sample data. Each sample has 40 million probes. Even a single chromosome has >3M probes. I tried some R-based and Matlab-based aCGH analysis so ...
acgh written 11.6 years ago by pingzhao Hu210 • updated 11.6 years ago by Sean Davis21k
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A friendly mention of LPE package
... Dear Users, If you use LPE package, this information may be helpful for you. Based on my experience, LPE package is very useful to identify differentially expressed genes for data sets with very small sample size. One thing that did not/not clearly document in the user manual is that when the sa ...
lpe written 11.7 years ago by pingzhao Hu210
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sample size estimation in genome wide association studies / packages
... Hi Alex, Here are some references: WJ Gauderman (2002), "Sample size requirements for matched case-control studies of gene-environment interaction", Stat Med 21:35-50. WJ Gauderman (2002), "Sample size requirements for association studies of gene-gene interaction", American Journal of Epidemiology ...
written 11.8 years ago by pingzhao Hu210
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sample size estimation in genome wide association studies / packages
... Hi Philippe, try Quanto software [1]http://hydra.usc.edu/GxE/ pingzhao ======================================== Pingzhao Hu Statistical Analysis Facility The Centre for Applied Genomics (TCAG) The Hospital for Sick Children Research Institute MaRS Centre - East Tower ...
written 11.8 years ago by pingzhao Hu210 • updated 11.8 years ago by alex lam RI310
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RES: LIMMA: load two-color data (Imagene format)
... Hi Leonardo, Thanks. The comments you suggested still do not work. > library (limma) > targets1 <- as.matrix(read.table("targets.txt", header = TRUE)); targets1 SlideNumber FileNameCy3 FileNameCy5 [1,] "12" "MB72-20-12_532.txt" "MB72-20-12_635.t ...
written 12.0 years ago by pingzhao Hu210 • updated 12.0 years ago by Leonardo Rocha40
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LIMMA: load two-color data (Imagene format)
... Hi, I have a two-colour data generated by Imagene image analysis. I have a trouble in loading the data to do normalization using limma. > library(limma) > targets<-readTargets("targets.txt") > targets SlideNumber FileNameCy3 FileNameCy5 1 12 MB72- ...
limma written 12.0 years ago by pingzhao Hu210 • updated 12.0 years ago by Leonardo Rocha40
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CGH segmentation algorithms (snapCGH package)
... Hi Joao, The STAC method may help you (http://cbil.upenn.edu/STAC/). If you want to combine the results from the 3 algorithms, the Fisher method can be used to combine the p-values obtained from STAC in each region and each algorithm. Pingzhao ======================================== Pingzhao Hu ...
written 12.0 years ago by pingzhao Hu210

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Popular Question 11.6 years ago, created a question with more than 1,000 views. For design matrix and lmFit problems in limma

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