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GLM Univariate

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E. Bernardo

GLM Univariate

(I apologize for cross posting)

The goal is to investigate the effects of "calcium spray solutions" on the height of plants. There were four groups of plants in the experiment. Let A be the control group while B, C and D comprised the experiemntal group There were three groups in the experimental group because each group of plants will be sprayed with water containing 1%, 2% and 3% of calcium. The control group was sprayed with fresh water ( 0% calcium). More over, for each group, plants were planted in the 3 pots, with two plants each pot.

The question is: To investigate if the calcium spray solutions affect the height of plants, I will use the GLM Univariate with the height as dependent variable and the group (A, B, C, D) as fixed factor. Do I include pot in the fixed factor?

Thank you.

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Marta Garcia-Granero

Re: GLM Univariate

Eins Bernardo wrote:

>
> The goal is to investigate the effects of "calcium spray solutions" on
> the height of plants. There were four groups of plants in the
> experiment. Let A be the control group while B, C and D comprised
> the experiemntal group There were three groups in the experimental
> group because each group of plants will be sprayed with water
> containing 1%, 2% and 3% of calcium. The control group was sprayed
> with fresh water ( 0% calcium). More over, for each group, plants
> were planted in the 3 pots, with two plants each pot.
>
> The question is: To investigate if the calcium spray solutions affect
> the height of plants, I will use the GLM Univariate with the height
> as dependent variable and the group (A, B, C, D) as fixed factor. Do
> I include pot in the fixed factor?
>
>
>
>
>
> ------------------------------------------------------------------------

I would include Pot as a random factor, nested within groups. With GLM
univariate you need to paste the syntax (don't click on OK) and edit the
last line to something like this:

UNIANOVA....
...
...
...
...
/DESIGN= Group Pot WITHIN Group.

HTH,
Marta GG

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Bruce Weaver

Re: GLM Univariate

Administrator

García-Granero wrote

Eins Bernardo wrote:
>
> The goal is to investigate the effects of "calcium spray solutions" on
> the height of plants. There were four groups of plants in the
> experiment. Let A be the control group while B, C and D comprised
> the experiemntal group There were three groups in the experimental
> group because each group of plants will be sprayed with water
> containing 1%, 2% and 3% of calcium. The control group was sprayed
> with fresh water ( 0% calcium). More over, for each group, plants
> were planted in the 3 pots, with two plants each pot.
>
> The question is: To investigate if the calcium spray solutions affect
> the height of plants, I will use the GLM Univariate with the height
> as dependent variable and the group (A, B, C, D) as fixed factor. Do
> I include pot in the fixed factor?
>
>
>
>
>
> ------------------------------------------------------------------------
I would include Pot as a random factor, nested within groups. With GLM
univariate you need to paste the syntax (don't click on OK) and edit the
last line to something like this:

UNIANOVA....
...
...
...
...
/DESIGN= Group Pot WITHIN Group.

HTH,
Marta GG

I think you would indicate the nesting of Pot within Group like this:

/DESIGN= Group Pot(Group).

Another option would be to use MIXED, which usually handles random variables better than UNIANOVA or GLM, it seems to me. And of course, you could treat Group as a continuous variable (or "covariate" in SPSS lingo) rather than as a categorical variable (or "factor").

HTH.

--
Bruce Weaver
bweaver@lakeheadu.ca
http://sites.google.com/a/lakeheadu.ca/bweaver/

"When all else fails, RTFM."

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Marta Garcia-Granero

Re: GLM Univariate

Bruce

This:

/DESIGN= Group Pot WITHIN Group.

And this:

/DESIGN= Group Pot(Group).

Are exactly the same.

I teach my students both ways, but I like the first because the nesting is clearer.

I also teach them MIXED, but they find it more complicated (got mixed...)

MGG

Bruce Weaver escribió:

> García-Granero wrote:
>
>> Eins Bernardo wrote:
>>
>>> The goal is to investigate the effects of "calcium spray solutions" on
>>> the height of plants. There were four groups of plants in the
>>> experiment. Let A be the control group while B, C and D comprised
>>> the experiemntal group There were three groups in the experimental
>>> group because each group of plants will be sprayed with water
>>> containing 1%, 2% and 3% of calcium. The control group was sprayed
>>> with fresh water ( 0% calcium). More over, for each group, plants
>>> were planted in the 3 pots, with two plants each pot.
>>>
>>> The question is: To investigate if the calcium spray solutions affect
>>> the height of plants, I will use the GLM Univariate with the height
>>> as dependent variable and the group (A, B, C, D) as fixed factor. Do
>>> I include pot in the fixed factor?
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>> I would include Pot as a random factor, nested within groups. With GLM
>> univariate you need to paste the syntax (don't click on OK) and edit the
>> last line to something like this:
>>
>> UNIANOVA....
>> ...
>> ...
>> ...
>> ...
>> /DESIGN= Group Pot WITHIN Group.
>>
>> HTH,
>> Marta GG
>>
>>
>>
>
> I think you would indicate the nesting of Pot within Group like this:
>
> /DESIGN= Group Pot(Group).
>
> Another option would be to use MIXED, which usually handles random variables
> better than UNIANOVA or GLM, it seems to me. And of course, you could treat
> Group as a continuous variable (or "covariate" in SPSS lingo) rather than as
> a categorical variable (or "factor").
>
> HTH.
>
>
> -----
> --
> Bruce Weaver
> [hidden email]
> http://sites.google.com/a/lakeheadu.ca/bweaver/
> "When all else fails, RTFM."
>
> NOTE: My Hotmail account is not monitored regularly.
> To send me an e-mail, please use the address shown above.
> --
> View this message in context: http://old.nabble.com/GLM-Univariate-tp27634701p27637402.html
> Sent from the SPSSX Discussion mailing list archive at Nabble.com.
>
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Bruce Weaver

Re: GLM Univariate

Administrator

García-Granero wrote

Bruce

This:

/DESIGN= Group Pot WITHIN Group.

And this:

/DESIGN= Group Pot(Group).

Are exactly the same.

I teach my students both ways, but I like the first because the nesting is clearer.

I also teach them MIXED, but they find it more complicated (got mixed...)

MGG

Hi Marta. I did not know that, but should have known better than to doubt you. ;-)
I've never seen the "A WITHIN B" format in the Help files--is it there somewhere?

Cheers,
Bruce

Marta Garcia-Granero

Re: GLM Univariate

Bruce Weaver wrote:

García-Granero wrote:

Bruce

This:

/DESIGN= Group Pot WITHIN Group.

And this:

/DESIGN= Group Pot(Group).


Are exactly the same.


Hi Marta.  I did not know that, but should have known better than to doubt
you.  ;-)
I've never seen the "A WITHIN B" format in the Help files--is it there
somewhere?

If you click on "Syntax help" icon after pasting UNIANOVA coomand, you can get this:

DESIGN Subcommand (UNIANOVA command)

.
.
.

To include a term for an interaction between factors, use the keyword BY or the asterisk (*) to join the factors involved in the interaction. For example, A*B means a two-way interaction effect of A and B, where A and B are factors. A*A is not allowed because factors inside an interaction effect must be distinct.

nested design,nested design,nested design

UNIANOVA command,UNIANOVA command,UNIANOVA command

To include a term for nesting one effect within another, use the keyword WITHIN or a pair of parentheses on the DESIGN subcommand. For example, A(B) means that A is nested within B. The expression A(B) is equivalent to the expression A WITHIN B. When more than one pair of parentheses is present, each pair of parentheses must be enclosed or nested within another pair of parentheses. Thus, A(B)(C) is not valid.

Best regards,
Marta

--
For miscellaneous SPSS related statistical stuff, visit:
http://gjyp.nl/marta/

E. Bernardo

Re: GLM Univariate

How about:

/DESIGN=Group SET Group*SET.

How is it differ with your syntax. Is that wrong?

--- On Thu, 2/18/10, García-Granero <[hidden email]> wrote:

From: García-Granero <[hidden email]>
Subject: Re: GLM Univariate
To: [hidden email]
Date: Thursday, 18 February, 2010, 5:08 PM
Bruce Weaver wrote:
García-Granero wrote:
  
Bruce

This:

/DESIGN= Group Pot WITHIN Group.

And this:

/DESIGN= Group Pot(Group).


Are exactly the same.


    
Hi Marta.  I did not know that, but should have known better than to doubt
you.  ;-)
I've never seen the "A WITHIN B" format in the Help files--is it there
somewhere?
  
If you click on "Syntax help" icon after pasting UNIANOVA coomand, you can get this:

DESIGN Subcommand (UNIANOVA command)
.
.
.

To include a term for an interaction between factors, use the keyword BY or the asterisk (*) to join the factors involved in the interaction. For example, A*B means a two-way interaction effect of A and B, where A and B are factors. A*A is not allowed because factors inside an interaction effect must be distinct.

nested design,nested design,nested design

UNIANOVA command,UNIANOVA command,UNIANOVA command

To include a term for nesting one effect within another, use the keyword WITHIN or a pair of parentheses on the DESIGN subcommand. For example, A(B) means that A is nested within B. The expression A(B) is equivalent to the expression A WITHIN B. When more than one pair of parentheses is present, each pair of parentheses must be enclosed or nested within another pair of parentheses. Thus, A(B)(C) is not valid.

Best regards,
Marta
--
For miscellaneous SPSS related statistical stuff, visit:
http://gjyp.nl/marta/

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Marta Garcia-Granero

Re: GLM Univariate

Eins Bernardo wrote:
> How about:
>
> /DESIGN=Group SET Group*SET.
>
> How is it differ with your syntax. Is that wrong?
>
Yes it is. If Pot (SET?) is nested within Group because you have two
random pots within each treatment group, then an interaction term is out
of the question (wrong from a design point of view: nested items can't
interact with their nesting factor).

Marta

--
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http://gjyp.nl/marta/

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Marta Garcia-Granero

Re: GLM Univariate

In reply to this post by E. Bernardo

Eins:

Perhaps I answered too fast because I misunderstood your first
description of the layout of your experiment. Tell me if I have the
correct picture.

You have 4 treatment groups (1 control, 3 increasing doses of Calcium).
Each treatment has 3 pots, and each pot has 2 plants.

Is that correct? If not, please describe you design with more detail
(whether the same pots have plants that receive different treatments,
for instance...).

Marta

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Marta Garcia-Granero

Re: GLM Univariate

In reply to this post by E. Bernardo

Eins Bernardo wrote:
> Why is the posthoc goes like that?
>

By default, SPSS uses the residual MS to compute Post-hoc tests. In a
nested design, since the F test is computed dividing MS(Group) by
MS(Set), you need that Post-hoc tests uses the same MS to compute the
SE(diff.) for the means comparisons.

HTH,
Marta

>
>
>
> Be careful when running POST-HOC comparisons for Group (in case of
> a significant result at Group level):
>
> /POSTHOC = Group ( TUKEY ) vs Set(Group)
> /DESIGN = Group Set(Group).
>
> Regards,
> Marta
>
> -- For miscellaneous SPSS related statistical stuff, visit:
> http://gjyp.nl/marta/
>

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E. Bernardo

Re: GLM Univariate

Dear Marta et al,

I followed your suggestion: The F-test is significant for both Group and SET(group) but the results of the posthoc unfortunately are insignificant. Can someone explain why?

The syntax is as follows:

UNIANOVA

height BY Group SET

/METHOD = SSTYPE(3)

/INTERCEPT = INCLUDE

/POSTHOC = Group ( TUKEY ) vs Set(Group)

/PLOT = PROFILE( Group Group*SET )

/CRITERIA = ALPHA(.05)

/DESIGN= Group SET(Group).

Eins

--- On Mon, 2/22/10, García-Granero <[hidden email]> wrote:

From: García-Granero <[hidden email]>
Subject: Re: GLM Univariate
To: [hidden email]
Date: Monday, 22 February, 2010, 7:27 AM

Eins Bernardo wrote:
> Why is the posthoc goes like that?
>

By default, SPSS uses the residual MS to compute Post-hoc tests. In a
nested design, since the F test is computed dividing MS(Group) by
MS(Set), you need that Post-hoc tests uses the same MS to compute the
SE(diff.) for the means comparisons.

HTH,
Marta

>
>
>
>    Be careful when running POST-HOC comparisons for Group (in case of
>    a significant result at Group level):
>
>    /POSTHOC = Group ( TUKEY ) vs Set(Group)
>    /DESIGN = Group Set(Group).
>
>    Regards,
>    Marta
>
>    -- For miscellaneous SPSS related statistical stuff, visit:
>    http://gjyp.nl/marta/
>

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E. Bernardo

Re: GLM Univariate

In reply to this post by Marta Garcia-Granero

Dear Marta,

What is the name of the Statistical method that you have suggested? Is it "between subjects ANOVA"

Eins

--- On Mon, 2/22/10, García-Granero <[hidden email]> wrote:

From: García-Granero <[hidden email]>
Subject: Re: GLM Univariate
To: [hidden email]
Date: Monday, 22 February, 2010, 7:27 AM

Eins Bernardo wrote:
> Why is the posthoc goes like that?
>

By default, SPSS uses the residual MS to compute Post-hoc tests. In a
nested design, since the F test is computed dividing MS(Group) by
MS(Set), you need that Post-hoc tests uses the same MS to compute the
SE(diff.) for the means comparisons.

HTH,
Marta

>
>
>
>    Be careful when running POST-HOC comparisons for Group (in case of
>    a significant result at Group level):
>
>    /POSTHOC = Group ( TUKEY ) vs Set(Group)
>    /DESIGN = Group Set(Group).
>
>    Regards,
>    Marta
>
>    -- For miscellaneous SPSS related statistical stuff, visit:
>    http://gjyp.nl/marta/
>

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Marta Garcia-Granero

Re: GLM Univariate

Hi

Eins Bernardo wrote:
>
> What is the name of the Statistical method that you have suggested? Is
> it "between subjects ANOVA"
>
>
Nested ANOVA.

Concerning your other question (Group effect significant but Post-Hoc
comparisons non significant), can you send the results?

Marta

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Marta Garcia-Granero

Re: GLM Univariate

In reply to this post by E. Bernardo

Eins Bernardo wrote:
> Dear Marta, et al.
>
> You wrote:
> >>Concerning your other question (Group effect significant but Post-Hoc
> comparisons non significant), can you send the results?
> >>Marta
>
> Please see attachment.
>

Since the design was balanced, I though it would not be necessary to
modify the sum of squares type to 1. With SPSS 15 it would have given
the same result, but I see that with 17 (or 18?) it has changed. Use
this syntax:

UNIANOVA
Stem_height BY Group SET
/METHOD = SSTYPE(1)
/INTERCEPT = INCLUDE
/POSTHOC = Group ( TUKEY ) vs Set(Group)
/PRINT=DESCRIPTIVE
/PLOT = PROFILE( Group )
/CRITERIA = ALPHA(.05)
/DESIGN= Group SET(Group).

Now the group effect will be non significant (as it should be, given the
small diferences between groups as compared to the random fluctuation
between Sets)

Marta

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Marta Garcia-Granero

Re: GLM Univariate

In reply to this post by E. Bernardo

Eins Bernardo wrote:
> I am using version 17. The group is still significant but none of the
> pairwise comparison is significant.
>
Now I realize, for the first time, that you are not treating Set as a
random factor. Try this modified version of the syntax:

UNIANOVA
Stem_height BY Group SET
/RANDOM=Set
/METHOD = SSTYPE(1)
/POSTHOC = Group ( TUKEY ) vs Set(Group)
/PRINT=DESCRIPTIVE
/PLOT = PROFILE( Group )
/DESIGN= Group SET(Group).

If it doesn't give the expected results, then I'll ask for help (from
the kind and nice SPSS support people that might be reading this).

Marta

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E. Bernardo

Re: GLM Univariate

Hi Marta, et al.

The problem was already solved. Thank you, Marta, for the solution.

I would like to raise the issue based on what I have discovered a few days back.

What is the statistical explaination of the instances wherein the ANOVA is highly significant but none of the posthoc test is significant? Assume that both GROUP and SET are "fixed factors".

Eins

--- On Tue, 2/23/10, García-Granero <[hidden email]> wrote:

From: García-Granero <[hidden email]>
Subject: Re: GLM Univariate
To: [hidden email]
Date: Tuesday, 23 February, 2010, 4:05 PM

Eins Bernardo wrote:
> I am using version 17. The group is still significant but none of the
> pairwise comparison is significant.
>
Now I realize, for the first time, that you are not treating Set as a
random factor. Try this modified version of the syntax:

UNIANOVA
Stem_height BY Group SET
/RANDOM=Set
/METHOD = SSTYPE(1)
/POSTHOC = Group ( TUKEY ) vs Set(Group)
/PRINT=DESCRIPTIVE
/PLOT = PROFILE( Group )
/DESIGN= Group SET(Group).

If it doesn't give the expected results, then I'll ask for help (from
the kind and nice SPSS support people that might be reading this).

Marta

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Marta Garcia-Granero

Re: GLM Univariate

Eins Bernardo wrote:

> Hi Marta, et al.
>
> The problem was already solved. Thank you, Marta, for the solution.
>
> I would like to raise the issue based on what I have discovered a few
> days back.
> What is the statistical explaination of the instances wherein
> the ANOVA is highly significant but none of the posthoc test is
> significant?
>

Swank, Paul R

Re: GLM Univariate

Scheffe's posttest comparison guarantees at least one significant follow-up test but it controls for all comparisons, both pairwise and complex. Posttest comparisons are not limited to pairwise tests.

Dr. Paul R. Swank,
Professor and Director of Research
Children's Learning Institute
University of Texas Health Science Center-Houston

-----Original Message-----
From: SPSSX(r) Discussion [mailto:[hidden email]] On Behalf Of Marta García-Granero
Sent: Tuesday, March 02, 2010 11:22 AM
To: [hidden email]
Subject: Re: GLM Univariate

Eins Bernardo wrote:

Post hoc tests focus on pairwise differences between means, while the
overall F tests whether there is any difference among any pair of
combination of means. For instance, the F could be significant because
mean1+mean2 combined differ significantly from mean3+mean4 combined. No
post hoc test would reveal that.

HTH,
Marta GG

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E. Bernardo

Re: GLM Univariate

In reply to this post by Marta Garcia-Granero

Marta wrote:

>>>Post hoc tests focus on pairwise differences between means, while the
overall F tests whether there is any difference among any pair of
combination of means. For instance, the F could be significant because
mean1+mean2 combined differ significantly from mean3+mean4 combined. No
post hoc test would reveal that.

Is the posthoc you are referring to is true also to post hoc in one-way anova?

--- On Tue, 3/2/10, Marta García-Granero <[hidden email]> wrote:

From: Marta García-Granero <[hidden email]>
Subject: Re: GLM Univariate
To: [hidden email]
Date: Tuesday, 2 March, 2010, 5:21 PM

Eins Bernardo wrote:

> Hi Marta, et al.
>
> The problem was already solved. Thank you, Marta, for the solution.
>
> I would like to raise the issue based on what I have discovered a few
> days back.
> What is the statistical explaination of the instances wherein
> the ANOVA is highly significant but none of the posthoc test is
> significant?
>
Post hoc tests focus on pairwise differences between means, while the
overall F tests whether there is any difference among any pair of
combination of means. For instance, the F could be significant because
mean1+mean2 combined differ significantly from mean3+mean4 combined. No
post hoc test would reveal that.

HTH,
Marta GG

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Marta Garcia-Granero

Re: GLM Univariate

Eins Bernardo wrote:

> Marta wrote:
> >>>Post hoc tests focus on pairwise differences between means, while the
> overall F tests whether there is any difference among any pair of
> combination of means. For instance, the F could be significant because
> mean1+mean2 combined differ significantly from mean3+mean4 combined. No
> post hoc test would reveal that.
>
> Is the posthoc you are referring to is true also to post hoc in
> one-way anova?
>

Beg your pardon? I don't understand the question. Anyway, what I said
about "classical post-hoc tests" (Tukey ...) is true for any ANOVA
design (ONEWAY, nested, repeated measures...).

Marta

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