Question

limma manual typo

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jeltje.van.baren • 0

@e09edacf

Last seen 2.0 years ago

United States

There's a duplicated word in the current limma userguide.pdf ('last revised 14 Nov 2021'), page 34:


(...)and Affymetrix arrays, include include con-
trol probes (...)

Btw this manual is a joy to read! Logical and clear, couldn't be any better.

limma • 807 views

ADD COMMENT • link updated 2.1 years ago by Gordon Smyth 52k • written 2.2 years ago by jeltje.van.baren • 0

score 0 · Answer 1 · 2022-10-28

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Gordon Smyth 52k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

Thanks very much. Now fixed.

ADD COMMENT • link 2.2 years ago Gordon Smyth 52k

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Jumping in here to report a small bug:

plotMD.SummarizedExperiment <- function(object, column=1, xlab="Average log CPM (this sample and others)", ylab="log-ratio (this sample vs others)", zero.weights=FALSE, prior.count=3, ...)
#   Created 03 April 2020.  Last modified 03 April 2020.
{
    y <- SE2DGEList(y)
    plotMD.DGEList(y, column=column, xlab=xlab, ylab=ylab, main=colnames(y)[column], status=y$genes$Status, zero.weights=zero.weights, prior.count=prior.count, ...)
}

Should be y <- SE2DGEList(object). Function currently errors with "y not found" for SummarizedExperiments.

ADD REPLY • link 2.1 years ago ATpoint ★ 4.6k

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Thanks very much, now fixed. The fix should make it into the Bioc 3.16 Release in a day or two.

ADD REPLY • link 2.1 years ago Gordon Smyth 52k