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 [[alternative HTML version deleted]]

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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}