[BioC] Mistake in the Limma documentation package read.maimages

[Gordon K Smyth]

Dear Duarte Molha,

Thanks the pointing out the typo.  The help page should say

source="agilent" now has the same meaning as "agilent.median" whereas 
previously it had same meaning as "agilent.mean"

I have now made the correction.

With a clear cut documentation error like this, you are welcome to write 
directly to the page author (me in this case) rather than to the mailing 
list.  But we are very grateful to get the correction either way.

Best wishes
Gordon

--------- original message --------
[BioC] Mistake in the Limma documentation package read.maimages
Duarte Molha Duarte.Molha at ogt.co.uk
Fri Oct 12 15:44:22 CEST 2012

Dear Developers

This is my first time writing to your mailing list and I apologise if this 
should be handled in another way .

I would like to report what I believe is a mistake in the documentation of 
the read.maimages package, part of the limma library.

On the second paragraph of the "Details" on the help section the Agilent 
Background estimates description is confusing and part of is has to be 
incorrect:

"...Background esimates are always medians. For Agilent, "agilent" or 
"agilent.median" use median foreground while "agilent.mean" uses mean 
foreground. (Note change of behavior from limma 3.11.17 onwards; "agilent" 
now has same meaning as "agilent.mean" whereas previously it had same 
meaning as "agilent.mean".)

Particularly the last sentence. It should either be :

agilent" now has same meaning as "agilent.median" whereas previously it 
had same meaning as "agilent.mean".)
agilent" now has same meaning as 
"agilent.mean" whereas previously it had same meaning as 
"agilent.median".)

I hope this helps,

Best regards,
Duarte Molha

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