User: Jain, Nitin

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Jain, Nitin70
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13 years, 6 months ago
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14 years, 9 months ago
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n*********@pfizer.com

Posts by Jain, Nitin

<prev • 7 results • page 1 of 1 • next >
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LPE question
... Dear Lisa, The function 'fdr.adjust' uses for loops in R, which are not very efficient. However, I have tried it on 64-bit Linux machine in Pfizer, and it runs quite fast (< 1 hr) for 1000-iterations. LPE is best suited if the number of replicates and samples are less than or equal to 5. We up ...
lpe written 13.5 years ago by Jain, Nitin70
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incoherence with LPE
... Hello Sabrina, The function "fdr.adjust" with "resamp" option gives the matrix showing the cutoff values of x-critical at different target fdrs. It is investigator's decision to choose the cutoff fdr - the function fdr.adjust will give you a "guideline" corresponding to the chosen fdr. You should ...
lpe written 14.0 years ago by Jain, Nitin70
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LPE method based on RMA vs. MAS5
... LPE pools the variance of genes showing similar intensities, so it is useful irrespective of the preprocessing step. Best, Nitin ______________________ Nitin Jain, PhD Non Clinical Statistics Pfizer, Inc. (Groton, CT) Bldg: 260, # 1451 Ph: (860) 686-2526 (Office) Fax: (860) 686-6170 -----Orig ...
preprocessing lpe written 14.0 years ago by Jain, Nitin70
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Answer: A: FDR adjustment in LPE
... Hi, In a recent paper submitted to BMC bioinformatics, we show that resampling based FDR adjustment method is better than BH method for small sample size. For small sample sizes, BH is quite conservative as shown in our simulation study. Will put the copy of the submitted paper at: http://www.heal ...
written 14.3 years ago by Jain, Nitin70
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LPE
... In LPE, rank-invariant resampling based FDR is used. For manuscript of the paper, please visist http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformati cs/ z-scores need not follow N(0,1) distribution. -N ______________________ Nitin Jain, PhD Non Clinical Statistics Pfizer, Inc. ...
cdf affy lpe assign written 14.5 years ago by Jain, Nitin70
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Answer: A: Help with LPE error message
... Could you please send me a subset of the data which caused this error? -Nitin nitin.jain@pfizer.com -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Puhong Gao Sent: Sunday, March 13, 2005 9:20 PM To: bioconductor@s ...
written 14.5 years ago by Jain, Nitin70
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Answer: A: LPE errors
... Hi Stephanie, Could you please let me know the error you are getting with MAS 5? The preprocessing function in LPE package is just IQR normalization and log (2) transformation, so you should be able to use any normalization method with LPE. Regards, -N ______________________ Nitin Jain, PhD Non C ...
written 14.7 years ago by Jain, Nitin70

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