[BioC] LIMMA: How do I get the standard deviation?

[Gordon Smyth]

>Date: Fri, 04 Feb 2005 00:21:04 +0100
>From: Sebastian Thieme <Tobar at gmx.de>
>Subject: [BioC] LIMMA: How do I get the standard deviation?
>To: bioconductor at stat.math.ethz.ch
>Message-ID: <6.2.0.14.0.20050204000430.02c8eeb0 at mail.gmx.net>
>Content-Type: text/plain; charset="us-ascii"; format=flowed
>
>Hello !
>
>To get the intensities of R and G channel I use RG.MA() on normalized data
>set.
>I can calculate the standard deviation using simple function sd( ). But
>there  the spot duplicates are not taken into account, only slide replicates.
>After running lmFit(), eBayes() and topTable() the duplicates are accounted.
>But how can I get from that results the standard deviation?

Standard deviation of what?

>Does it correspond to $stdev.unscaled from lmFit() output and can I use
>that for simple graphics (like R to G channel with sd-bars)?

sd-bars of what?

Gordon

>Thanks !
>
>Sebastian Thieme