[BioC] Type III Sum of Squares Calculation

[Man, Michael]

Yes, you can use either Perl or R to do automate the task.  The key is to
get your data in the right format.  Use apply() when you need do large
number of loops because it will save the computing time.  

You may want to try library(RODBC) for DB connectivity.  

Michael

 -----Original Message-----
From: 	Subramanian Karthikeyan [mailto:Subramanian_Karthikeyan at hc-sc.gc.ca]

Sent:	Wednesday, October 22, 2003 12:08 PM
To:	Man, Michael
Cc:	bioconductor at stat.math.ethz.ch
Subject:	RE: [BioC] Type III Sum of Squares Calculation


Thanks Mike,

Is there a way of automating the task (e.g. using Perl  or within R itself,
maybe using a loop or something like that, so that I can I do a
high-throughput analysis of several datasets, and then output/export the
result tables in an excel spreadsheet?

Any hint would be useful.

Thanks again,
Karth.




 

                      "Man, Michael"

                      <Michael.Man at pfiz        To:       "'Subramanian
Karthikeyan'" <Subramanian_Karthikeyan at hc-sc.gc.ca>,            
                      er.com>
bioconductor at stat.math.ethz.ch

                                               cc:

                      2003-10-22 08:30         Subject:  RE: [BioC] Type III
Sum of Squares Calculation                                
                      AM

 

 





Hope this helps.  -michael

calculating type III SS
 Use Anova(lm, type = "III") in the "car" package
          C:\Program Files\R\rw1031\library\car\html\Anova.html

 (below is from Brian D. Ripley)
 Yes, but we don't tell you how to avoid leading you into a mire. See

 http://www.stats.ox.ac.uk/pub/MASS3/Exegeses.pdf.
 Most of the time drop1() does what people are using `Type III' for.
          (C:\Program Files\R\rw1031\library\base\html\add1.html)


 -----Original Message-----
From:       Subramanian Karthikeyan
[mailto:Subramanian_Karthikeyan at hc-sc.gc.ca]

Sent: Tuesday, October 21, 2003 8:09 AM
To:   bioconductor at stat.math.ethz.ch
Subject:    [BioC] Type III Sum of Squares Calculation

HI All:

Can anyone give me the formulae/steps for calculating the type III sum of
squares for an unbalanced 2-way ANOVA design?  Eg. we are looking at 8
treatments x 4 doses, with unequal numbers of replications within the
groups.  I really need the stepwise calculation, as I would try to put it
in my own code (possibly in Visual Basic) to automate the task.

Thanks very much.

Karth.




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