User: Nitin Jain

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Nitin Jain30
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15 years, 3 months ago
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15 years, 8 months ago
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n***@virginia.edu

Posts by Nitin Jain

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Answer: A: number of Replicates - Fold change vs Limma or Siggenes/SAM
... Try the Local Pooled error (LPE) test on Bioconductor. Reference: http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformati cs/research/LPE.pdf -Nitin On Sat, 22 May 2004 14:17:19 -0400 "Luckey, John" wrote: > >I am looking to identify differentially expressed genes >from ...
written 15.3 years ago by Nitin Jain30
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Answer: A: problem with LPE
... Dear Philippe, As the warning messages indicate, NANs are being produced in taking square root, which means some values in var.x are being calculated as negative from baseOlig.error function. I apply preprocess function to the data set, before giving it as input for baseOlig.error function, which t ...
written 15.5 years ago by Nitin Jain30
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Comment: C: ttest or fold change
... You may try LPE (under developmental packages on Bioconductor), which is suited for significance analysis for low number of replicates. Regards, -Nitin > > Hi, > > My own calculations have also shown a lack of sensitivity of both > t-testing and other approaches when we have few rep ...
written 15.7 years ago by Nitin Jain30

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