[R] ANOVA and LSD TEST - contrasting results

[John Sorkin]

Roberto,
Please be more specific. What are the differences between ANOVA and LSD that give you concern?
John

John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)

>>> Roberto <rmoscetti at unitus.it> 11/19/2011 6:10 AM >>>
Dear all,
concerne to my issue, I obtained different results between ANOVA and LSD
TEST (agricolae package), and I ask me why




>anova <- aov(SS ~ Treatment*Lot)
>summary(anova)

                     Df    Sum Sq   Mean Sq F value Pr(>F)
Treatment           7 0.0000534 7.622e-06   1.107  0.374
Lot            2 0.0000059 2.954e-06   0.429  0.654
Treatment:Lot 14 0.0001038 7.412e-06   1.077  0.401
Residuals            48 0.0003304 6.883e-06    

> LSD.test(anova, "Treatment")

Study:

LSD t Test for SS 

Mean Square Error:  6.883013e-06 

Trattamento,  means and individual ( 95 %) CI

            SS      std.err replication        LCL        UCL
A30 0.02966558 0.0019037856           9 0.02583776 0.03349340
AM  0.02844520 0.0005186885           9 0.02740230 0.02948809
C30 0.02913658 0.0006792219           9 0.02777092 0.03050225
CM  0.02964944 0.0005398926           9 0.02856391 0.03073496
T30 0.02979624 0.0006920447           9 0.02840479 0.03118769
TS  0.02891764 0.0004981543           9 0.02791603 0.02991924
V30 0.03112188 0.0005157621           9 0.03008487 0.03215889
VM  0.03087886 0.0006874520           9 0.02949664 0.03226107

alpha: 0.05 ; Df Error: 48
Critical Value of t: 2.010635 

Least Significant Difference 0.002486659
Means with the same letter are not significantly different.

Groups, Treatments and means
a        A1     0.03112188 
ab       A2      0.03087886 
ab       B1     0.02979624 
ab       C1     0.02966558 
ab       D1      0.02964944 
ab       D2     0.02913658 
ab       B2      0.02891764 
 b       C2      0.0284452 

how is it possible? my mistake to set anova?

Best regards,
Roberto


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