Question

This experiment was designed originally to sample various meat and carcass quality 
aspects of Ontario pigs from 1990 to 1993. It wasn’t designed to detect QTL associated 
with meat quality characteristics of pork, but we had enough meat samples remaining 
from this experiment to have DNA that we could add this component. The population was an outbred population. 
Moisture retained by meat has a connection with the flavour and juiciness of the cooked 
product. The results below are from an analysis of drip loss (moisture lost from a fresh 
piece of pork in 24 hours) and genotypes derived from the meat samples.

In this population, the polymorphism that was detected was labelled MspI (which is a pituitary transcription factor
gene), and the genotypes were labelled 1 = A1A1, 2 = A1A2 and 3 = A2A2. The allele frequencies were 
f(A1) = 0.68 and f(A2) = 0.32. Although the genotypic frequencies were not exactly p2, 
2pq and q2, for the purposes of this lab, you can assume they were. The model for this 
analysis included hot carcass weight (HOTCWT1) to adjust for carcass size differences, 
the test barn fill number (FILLNO) to account for known environmental factors, sex 
(males, females and barrows – castrated males). Drip loss is measured in percentage and 
less drip loss is better (more moisture retained in the meat).
Some important information is contained in the printout below. 
This is an output from SAS. The statistical tests in SAS are all accompanied by 
probability values (probability of a larger F value, "Pr > F" and larger t value, "Pr > |t|"). 
This is a p-value and to make a statistical test, you compare these probabilities to the 
critical value you have established for the experiment. If the Pr > F is less than your 
critical value (I recommend using 0.05 as your critical value) then the factor being tested is significant.
The Pr > |t| column tests the difference of means from zero so factors with this column are being 
tested as significantly different from zero. “LSMeans” refers to an adjusted mean (average) that is 
used as a measure of the average of each factor in the model, including the genotypes. As 
noted above, the Pr > |t| column tests the difference of each LSMean from zero.

The GLM Procedure 

Dependent Variable: DLLNPCT which is Loin Drip Loss % 

                                     Sum of 

Source                     DF        Squares    Mean Square   F Value   Pr > F 

Model                      36    1564.325289      43.453480      3.53   <.0001 
Error                     211    2593.732982      12.292573                    
Corrected Total           247    4158.058271  

                                 
R-Square     Coeff Var      Root MSE    DLLNPCT Mean 
0.376215      29.25578      3.506077        11.98422 

Source                     DF      Type III SS   Mean Square   F Value   Pr > F 

HOTCWT1                     1     32.8255304     32.8255304      2.67   0.1037 
FILLNO                     22    714.3077354     32.4685334      2.64   0.0002 
SEX                         2     47.9965480     23.9982740      1.95   0.1445 
MspI                        2    189.9263802     94.9631901      7.73   0.0006 

Standard 
Parameter               Estimate             Error    t Value    Pr > |t| 

Intercept            7.223163310 B      5.42727411       1.33      0.1847 
HOTCWT1              0.075560897        0.04623945       1.63      0.1037 
SEX       B          1.136799775 B      0.61026699       1.86      0.0639 
SEX       F          0.841730577 B      0.56550265       1.49      0.1381 
SEX       M          0.000000000 B       .                .         .     
MspI      1         -3.836074399 B      1.23681260      -3.10      0.0022 
MspI      2         -2.910062857 B      1.09289797      -3.49      0.0006 
MspI      3          0.000000000 B       .                .         .     

Least Squares Means 
MspI         DLLNPCT        Standard 
             LSMEAN           Error    Pr > |t| 

1        13.2747909       0.5631372      <.0001 

2        10.3647280       1.0321316      <.0001 

3         9.4387165       1.1460667      <.0001 

Refer to the SAS output sample from question 1 above. Based on a t-test of the difference of a value from zero, which parameters were statistically significantly different from zero?

Question 2 options:

	1) Hot Carcass Weight
	2) Sex B (Barrows) and Sex F (Females)
	3) Intercept and hot carcass weight
	4) MSP1 genotypes 1 and 2
	5) The intercept

Answer 1

since p value for MSPL are less than 0.05 , this is statistically significantly different from zero

Correct option is : 4) MSP1 genotypes 1 and 2