[BioC] Re: funnction in LIMMA

[Gordon Smyth]

Dear Ping,

I do not know the paper by Calinksi & Harabasz (1974), but the function 
'bwss' simply does one-way analysis of variance as explained in any 
introductory statistics text.

I did not actually intend the 'bwss' function to be used for differential 
expression analyses as you describe. It is there rather as a utility 
function for the 'anova' function for MAList objects. However you could use 
it for your data by setting 'x' to be a vector of log-ratios or 
log-intensities and 'group' to be a vector which takes value '1' for 
group1, '2' for group2 etc etc. I cannot tell though whether this would be 
a sensible analysis for your data.

Best wishes
Gordon

At 03:07 PM 10/06/2003, you wrote:
>Dear Dr. Smyth,
>
>I am interested in your R package LIMMA.
>I want to use the function BWSS in this package, but
>I am not sure the meanings of the arguments of this function
>
>bwss <- function(x,group).
>
>Your docu. explains they are:
>
>x:     a numeric vector giving the responses.
>group: a vector or factor giving the grouping variable.
>
>For example, I have a microaray dataset.
>gene1, .., gene 10 are grouped to group 1
>gene11,...,gene 20 are grouped to group 2
>gene21,.., gene 31 are grouped to group 3.
>
>The tumors are t1, t2, .., t10.
>
>For this dataset, how can I decide these two arguments: x and group????
>
>
>By the way, the meanings of sums of squares between the group means (bss)
>and sums of squares within the groups (wss) are the same as those
>in Calinski & Harabasz (1974) CH(K)=(B(k)/(k-1)) / (W(k)/(n-k))?????
>
>Your kind help is highly appreciated!!!!
>
>Best regards,
>
>ping

---------------------------------------------------------------------------------------
Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3050, Australia
Tel: (03) 9345 2326, Fax (03) 9347 0852,
Email: smyth at wehi.edu.au, www: http://www.statsci.org