User: stephane.cauchi

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Posts by stephane.cauchi

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How to control p-value inflation with limma
... Dear all, Using the limma package I compared the mRNA expression profiles between small groups (N=5) of isogenic mice (balb/c) for different conditions (Agilent one-color microarrays). I could observe strong p-value inflation (as measured by lambda) in most comparisons despite the FDR correction. O ...
limma pvalue inflation bacon written 2.1 years ago by stephane.cauchi0 • updated 2.1 years ago by Aaron Lun23k
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Answer: A: Get back to individual measures to calculate coefficients like the lmFit fucntio
... Thank you very much Aaron, Actually, if I don't take into account the attributed weights the resulting logFC may be quite different from what I get with lmFit. When using the above example, I get -0.0807573981440699 if the weights are taken into account and 0.0813813767914962 if they are not. Even ...
written 2.1 years ago by stephane.cauchi0
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Get back to individual measures to calculate coefficients like the lmFit fucntion (limma package)
... Hi ! I need to compare the transcriptome of 5 cases and 5 controls using one-color Agilent microarrays. Weights were computed by the following function: #My weight function myFlagFun <- function(x) { #Weight only strongly positive spots 1, everything else 0 present <- x$gIsPosAndSignif == 1 ...
limma lmfit weight individual written 2.1 years ago by stephane.cauchi0

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