Date: Mon, 7 Mar 2011 13:38:51 -0800
Reply-To: Bruce Weaver <bruce.weaver@hotmail.com>
Sender: "SPSSX(r) Discussion" <SPSSX-L@LISTSERV.UGA.EDU>
From: Bruce Weaver <bruce.weaver@hotmail.com>
Subject: Re: Anova SS1 vSS3 (using v 17.0)
In-Reply-To: <1299516429121-3412719.post@n5.nabble.com>
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I've now had time to take another look at this. It seems to me that both
Method (aka "assay") and Replicate are within-Ss (or repeated measures)
factors, with 2 and 3 levels respectively. It is also clear that ALIQUOT is
completely confounded with ID. If all of this is correct, then have a 2x3
repeated measures ANOVA, with repeated measures on both factors. To run
that model in the usual fashion, you have to restructure the data from LONG
to WIDE.
data list list / Row id (2f5.0) aliquot(a1) assay rep (2f2.0) kt lkt
(2f8.2).
begin data
151. 26 A 1 1 44.550 1.648848
152. 26 A 1 2 39.230 1.593615
153. 26 A 1 3 27.186 1.434345
154. 26 A 2 4 37.453 1.573482
155. 26 A 2 5 49.918 1.698259
156. 26 A 2 6 38.341 1.583661
169. 29 B 1 1 13.450 1.128722
170. 29 B 1 2 6.879 .8375258
171. 29 B 1 3 5.764 .7607239
172. 29 B 2 4 13.116 1.117787
173. 29 B 2 5 11.543 1.062301
174. 29 B 2 6 11.044 1.043127
181. 31 C 1 1 11.400 1.056905
182. 31 C 1 2 6.657 .8233027
183. 31 C 1 3 6.375 .8044802
184. 31 C 2 4 10.415 1.017641
185. 31 C 2 5 11.371 1.055816
186. 31 C 2 6 10.770 1.032208
199. 34 D 1 1 10.161 1.006936
200. 34 D 1 2 5.089 .7066036
201. 34 D 1 3 6.668 .8239956
202. 34 D 2 4 10.955 1.039603
203. 34 D 2 5 12.827 1.108116
204. 34 D 2 6 9.793 .9909264
211. 36 E 1 1 17.000 1.230449
212. 36 E 1 2 10.942 1.039088
213. 36 E 1 3 10.096 1.004149
214. 36 E 2 4 16.018 1.204596
215. 36 E 2 5 13.289 1.123484
216. 36 E 2 6 16.138 1.207857
end data.
* GLM Repeated Measures needs WIDE file format, so restructure.
CASESTOVARS
/ID=id
/INDEX=assay rep
/DROP = row
/GROUPBY=VARIABLE.
* Try model with ALIQUOT as a Between-Ss factor.
GLM lkt.1.1 lkt.1.2 lkt.1.3 lkt.2.4 lkt.2.5 lkt.2.6 BY aliquot
/WSFACTOR=method 2 Polynomial rep 3 Polynomial
/METHOD=SSTYPE(3)
/EMMEANS=TABLES(aliquot)
/EMMEANS=TABLES(method)
/EMMEANS=TABLES(rep)
/EMMEANS=TABLES(aliquot*method)
/EMMEANS=TABLES(aliquot*rep)
/EMMEANS=TABLES(method*rep)
/EMMEANS=TABLES(aliquot*method*rep)
/CRITERIA=ALPHA(.05)
/WSDESIGN=method rep method*rep
/DESIGN=aliquot.
* That model does not work, because ALIQUOT is completely
* confounded with ID -- i.e., there is only one ID for
* each level of ALIQUOT.
* Run the model without the Between-Ss factor ALIQUOT.
GLM lkt.1.1 lkt.1.2 lkt.1.3 lkt.2.4 lkt.2.5 lkt.2.6
/WSFACTOR=method 2 Polynomial rep 3 Polynomial
/METHOD=SSTYPE(3)
/PLOT=PROFILE(rep*method)
/EMMEANS=TABLES(method)
/EMMEANS=TABLES(rep)
/EMMEANS=TABLES(method*rep) compare(rep) adj(bonferroni)
/CRITERIA=ALPHA(.05)
/WSDESIGN=method rep method*rep.
HTH.
Bruce Weaver wrote:
>
> Your UNIANOVA syntax lists "method" as one of the factors, but "method" is
> not included in the description of the data. Are "assay" and "method"
> referring to the same variable?
>
> Also, UNIANOVA treats the 6 replicates per ID as if they are independent
> observations. But if they are repeated measures on the same unit (ID),
> then they will not be completely independent of each other, and should be
> treated accordingly. One way to do that is via a mixed design
> (between-within, or split-plot) ANOVA (Analyze - GLM - Repeated Measures).
> For this approach, you would have to restructure the data to have one row
> per ID, with the 6 replicates appearing in 6 columns. (Look up
> CASESTOVARS to see how to restructure the data.)
>
> HTH.
>
>
>
> Allan Reese (Cefas) wrote:
>>
>> I have a completely balanced dataset and fit the main effects only using
>> default (type 3) sums of squares. It reports 0df and 0ss for a factor
>> with two levels. Switching to type 1 sums of squares, it gives 1df and
>> a sensible sum of squares. Is there a simple reason why sstype(3)
>> should be so ornery?
>>
>> On a point of terminology, are SPSS hierarchical sums of squares
>> identical to SAS sequential ss?
>>
>> Data:
>> Row id aliquot assay rep kt lkt (the response)
>> 151. 26 A 1 1 44.550 1.648848
>> 152. 26 A 1 2 39.230 1.593615
>> 153. 26 A 1 3 27.186 1.434345
>> 154. 26 A 2 4 37.453 1.573482
>> 155. 26 A 2 5 49.918 1.698259
>> 156. 26 A 2 6 38.341 1.583661
>> 169. 29 B 1 1 13.450 1.128722
>> 170. 29 B 1 2 6.879 .8375258
>> 171. 29 B 1 3 5.764 .7607239
>> 172. 29 B 2 4 13.116 1.117787
>> 173. 29 B 2 5 11.543 1.062301
>> 174. 29 B 2 6 11.044 1.043127
>> 181. 31 C 1 1 11.400 1.056905
>> 182. 31 C 1 2 6.657 .8233027
>> 183. 31 C 1 3 6.375 .8044802
>> 184. 31 C 2 4 10.415 1.017641
>> 185. 31 C 2 5 11.371 1.055816
>> 186. 31 C 2 6 10.770 1.032208
>> 199. 34 D 1 1 10.161 1.006936
>> 200. 34 D 1 2 5.089 .7066036
>> 201. 34 D 1 3 6.668 .8239956
>> 202. 34 D 2 4 10.955 1.039603
>> 203. 34 D 2 5 12.827 1.108116
>> 204. 34 D 2 6 9.793 .9909264
>> 211. 36 E 1 1 17.000 1.230449
>> 212. 36 E 1 2 10.942 1.039088
>> 213. 36 E 1 3 10.096 1.004149
>> 214. 36 E 2 4 16.018 1.204596
>> 215. 36 E 2 5 13.289 1.123484
>> 216. 36 E 2 6 16.138 1.207857
>>
>>
>> UNIANOVA lkt BY aliquot method replicate
>> /METHOD=SSTYPE(1)
>> /INTERCEPT=INCLUDE
>> /EMMEANS=TABLES(method)
>> /CRITERIA=ALPHA(.01)
>> /DESIGN=method aliquot replicate.
>>
>> Univariate Analysis of Variance
>>
>> Notes
>> |-------------------------------|---------------|
>> |Output Created |07-Mar-2011 15:|
>> | |25:24 |
>> |-------------------------------|---------------|
>> |Comments | |
>> |---------------|---------------|---------------|
>> |Input |Active Dataset |DataSet0 |
>> | |---------------|---------------|
>> | |Filter | |
>> | |---------------|---------------|
>> | |Weight | |
>> | |---------------|---------------|
>> | |Split File | |
>> | |---------------|---------------|
>> | |N of Rows in |30 |
>> | |Working Data | |
>> | |File | |
>> |---------------|---------------|---------------|
>> |Missing Value |Definition of |User-defined |
>> |Handling |Missing |missing values |
>> | | |are treated as |
>> | | |missing. |
>> | |---------------|---------------|
>> | |Cases Used |Statistics are |
>> | | |based on all |
>> | | |cases with |
>> | | |valid data for |
>> | | |all variables |
>> | | |in the model. |
>> |---------------|---------------|---------------|
>> |Syntax |UNIANOVA lkt |
>> | |BY aliquot |
>> | |method |
>> | |replicate |
>> | |/METHOD=SSTYPE |
>> | |(1) |
>> | |/INTERCEPT=INCL|
>> | |UDE |
>> | |/EMMEANS=TABLES|
>> | |(method) |
>> | | |
>> | |/CRITERIA=ALPHA|
>> | |(.01) |
>> | | |
>> | |/DESIGN=method |
>> |---------------|---------------|---------------|
>> |Resources |Processor Time |0:00:00.016 |
>> | |---------------|---------------|
>> | |Elapsed Time |0:00:00.031 |
>> |---------------|---------------|---------------|
>>
>>
>>
>> [DataSet0]
>>
>>
>> Between-Subjects Factors
>> |--------------|--|
>> | |N |
>> |---------|----|--|
>> |aliquot |A |6 |
>> | |----|--|
>> | |B |6 |
>> | |----|--|
>> | |C |6 |
>> | |----|--|
>> | |D |6 |
>> | |----|--|
>> | |E |6 |
>> |---------|----|--|
>> |method |1.00|15|
>> | |----|--|
>> | |2.00|15|
>> |---------|----|--|
>> |replicate|1.00|5 |
>> | |----|--|
>> | |2.00|5 |
>> | |----|--|
>> | |3.00|5 |
>> | |----|--|
>> | |4.00|5 |
>> | |----|--|
>> | |5.00|5 |
>> | |----|--|
>> | |6.00|5 |
>> |---------|----|--|
>>
>>
>>
>> Tests of Between-Subjects Effects
>> Dependent Variable:lkt
>> |---------------|---------------|--|-----------|---------|----|
>> |Source |Type I Sum of |df|Mean Square|F |Sig.|
>> | |Squares | | | | |
>> |---------------|---------------|--|-----------|---------|----|
>> |Corrected Model|2.056a |9 |.228 |61.462 |.000|
>> |---------------|---------------|--|-----------|---------|----|
>> |Intercept |37.988 |1 |37.988 |10219.052|.000|
>> |---------------|---------------|--|-----------|---------|----|
>> |method |.128 |1 |.128 |34.418 |.000|
>> |---------------|---------------|--|-----------|---------|----|
>> |aliquot |1.743 |4 |.436 |117.219 |.000|
>> |---------------|---------------|--|-----------|---------|----|
>> |replicate |.185 |4 |.046 |12.466 |.000|
>> |---------------|---------------|--|-----------|---------|----|
>> |Error |.074 |20|.004 | | |
>> |---------------|---------------|--|-----------|---------|----|
>> |Total |40.119 |30| | | |
>> |---------------|---------------|--|-----------|---------|----|
>> |Corrected Total|2.131 |29| | | |
>> |---------------|---------------|--|-----------|---------|----|
>> a. R Squared = .965 (Adjusted R Squared = .949)
>>
>> [method+aliquot+replicate ss sum to model ss]
>>
>>
>> Estimated Marginal Means
>>
>> method
>> Dependent Variable:lkt
>> |------|----|----------|---------------------------|
>> |method|Mean|Std. Error|99% Confidence Interval |
>> | | | | |
>> | | | |---------------|-----------|
>> | | | |Lower Bound |Upper Bound|
>> |------|----|----------|---------------|-----------|
>> |1.00 |.a |. |. |. |
>> |------|----|----------|---------------|-----------|
>> |2.00 |.a |. |. |. |
>> |------|----|----------|---------------|-----------|
>> a. This modified population marginal mean is not estimable.
>>
>>
>>
>> UNIANOVA lkt BY aliquot method replicate
>> /METHOD=SSTYPE(3)
>> /INTERCEPT=INCLUDE
>> /EMMEANS=TABLES(method)
>> /CRITERIA=ALPHA(.01)
>> /DESIGN=method aliquot replicate.
>>
>>
>>
>>
>> Tests of Between-Subjects Effects
>> Dependent Variable:lkt
>> |---------------|---------------|--|-----------|---------|----|
>> |Source |Type III Sum |df|Mean Square|F |Sig.|
>> | |of Squares | | | | |
>> |---------------|---------------|--|-----------|---------|----|
>> |Corrected Model|2.056a |9 |.228 |61.462 |.000|
>> |---------------|---------------|--|-----------|---------|----|
>> |Intercept |37.988 |1 |37.988 |10219.052|.000|
>> |---------------|---------------|--|-----------|---------|----|
>> |method |.000 |0 |. |. |. |
>> |---------------|---------------|--|-----------|---------|----|
>> |aliquot |1.743 |4 |.436 |117.219 |.000|
>> |---------------|---------------|--|-----------|---------|----|
>> |replicate |.185 |4 |.046 |12.466 |.000|
>> |---------------|---------------|--|-----------|---------|----|
>> |Error |.074 |20|.004 | | |
>> |---------------|---------------|--|-----------|---------|----|
>> |Total |40.119 |30| | | |
>> |---------------|---------------|--|-----------|---------|----|
>> |Corrected Total|2.131 |29| | | |
>> |---------------|---------------|--|-----------|---------|----|
>> a. R Squared = .965 (Adjusted R Squared = .949)
>>
>>
>>
>> Estimated Marginal Means
>>
>> method
>> Dependent Variable:lkt
>> |------|----|----------|---------------------------|
>> |method|Mean|Std. Error|99% Confidence Interval |
>> | | | | |
>> | | | |---------------|-----------|
>> | | | |Lower Bound |Upper Bound|
>> |------|----|----------|---------------|-----------|
>> |1.00 |.a |. |. |. |
>> |------|----|----------|---------------|-----------|
>> |2.00 |.a |. |. |. |
>> |------|----|----------|---------------|-----------|
>> a. This modified population marginal mean is not estimable.
>>
>> [model ss does not equal sum of parts]
>>
>>
>> Thanks for any comments
>> Allan
>>
>>
>>
>>
>>
>> R Allan Reese
>> Senior statistician, Cefas
>> The Nothe, Weymouth DT4 8UB
>>
>> Tel: +44 (0)1305 206614 -direct
>> Fax: +44 (0)1305 206601
>>
>> www.cefas.co.uk
>> ***********************************************************************************
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>
-----
--
Bruce Weaver
bweaver@lakeheadu.ca
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.
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