Hi Indrajit and Bert,

I really appeciate your help.  I have coded as you mentioned, but I feel
like I am losing a lot of data because I am not accounting for the replicate
tanks (what if the 5 replicates of the same cross type vary more among tanks
than within?).  Below is what my data would look like (if it comes through)

   obs  male female rep response 1 1 1 1 34 2 1 1 1 44 . . . . . . . . . .
51 1 1 2 37 . . . . . . . . . . 251 1 2 1 42

So if I understand correctly, the five replicate tanks of each cross cannot
be treated as technical replicates?  They are not exactly repeated measures
in the sense they are different individuals in different replicate tanks.
If I pool all 250 observations for each cross, instead of treating it as
5x50 observations, I feel like I am losing a lot of information.

Austin


On Mon, Sep 26, 2011 at 11:40 PM, Indrajit Sengupta <indra_calisto@yahoo.com
> wrote:

>  Hi Paul,
>
> There should not be any problem. Here is how I visualize the data table
> looks like:
>
>      Obs Male_type
> Female_type
> Response 1 1 1 34 2 1 1 44 3 1 2 38 … … … …
> If your data frame has the above structure, R will automatically understand
> that there is replication. Your model form will remain the same.
>
> Regards,
> Indrajit
>
>   ------------------------------
> *From:* Austin Paul <austinpa@usc.edu>
> *To:* Indrajit Sengupta <indra_calisto@yahoo.com>
> *Cc:* "r-help@r-project.org" <r-help@r-project.org>
> *Sent:* Tuesday, September 27, 2011 10:57 AM
> *Subject:* Re: [R] two-way anova help
>
> Hi,
>
> Yes.  As I explained, the three male and three female types were crossed in
> all combinations (9 ways).  For each of the 9 types, I have *5 replicate
> tanks* (45 total tanks).  And from each of the 45 tanks I have 50
> observations for size.  So the 5 replicates are somehow nested within the
> two-way interaction?  If there was just 1 tank for each of the 9 crosses,
> yes, it would be very easy to code the two-way anova.  It may still be very
> easy, but I'm not quite sure how to account for the replicate tanks.
>
> Hope this makes more sense.
>
> Austin
>
>
>
> On Mon, Sep 26, 2011 at 10:21 PM, Indrajit Sengupta <
> indra_calisto@yahoo.com> wrote:
>
>  Can you explain what do you mean by "5 replicate tanks"?
>
> Doing a two way anova is very simple in R. You would need to fit a linear
> model (lm function).
>
> Eg.:
>
> > model <- lm(y ~ male + female + male:female, data =)
>
>
> Regards,
> Indrajit
>
>
>  ------------------------------
> *From:* Austin Paul <austinpa@usc.edu>
> *To:* r-help@r-project.org
> *Sent:* Tuesday, September 27, 2011 6:13 AM
> *Subject:* [R] two-way anova help
>
> Hello,
>
> I am having some trouble coding a two-way anova due to replicated
> treatments.
>
> I have a factorial design with three male parents and three female parents.
> They were mated in all combinations and their babies were grown out and
> measured for size.  50 babies were measured for each of the 9 crosses.  If
> I
> stopped here, I would have no troubles.  But I also have 5 replicate tanks
> for each of the 9 crosses.  My question is how to I code in the 5 replicate
> tanks per treatment?
>
> Thanks,
> Austin
>
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>
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>
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