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0
votes
0answers
18 views

Interaction with contrast and dummy coding

I have a question regarding the interpretation of an interaction using categorical variables where one is dummy coded (0, 1) and the other is contrast coded. The variables are: Var1: 3 levels, ...
0
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0answers
6 views

Specifying interaction contrasts for within x between terms in SPSS

I am trying to analyse a dataset with 3 groups of subjects and one repeated measure with 6 levels (accuracy at identifying 6 different emotions). I am using the GLM command from SPSS to do this, which ...
1
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0answers
35 views

How to create dummy variables for interaction term between categorical variables?

I'm building a logistic regression model estimating the probability of hospitalization based on several predictor variables, including indicator variables for various diagnosis categories (coded as ...
2
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0answers
26 views

Possible to code contrasts comparing each level to grand mean with no reference category?

I'm working on a health care outcome regression model using the deviation contrast scheme described on the UCLA SAS help page here for a collection of dichotomous predictor variables measuring medical ...
1
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2answers
60 views

Forcing nlme to give the results for the levels of a treatment as “absolute” values instead of contrasts

I am using a nonlinear model to fit an equation to data using nlme in R. Several values (one by treatment) are estimated for a fixed effect. As usual, by default ...
0
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1answer
28 views

Refitting with different contrasts vs. pairwise comparisons

Say, I fit a linear or generalised linear model in R with dummy coding (contr.treatment for ...
0
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0answers
33 views

How to do planned comparisons on repeated measures (GLM repeated measures) using SPSS?

I have issues figuring out how to perform planned comparisons using a GLM for repeated measures analysis. More specifically, I have one group of subjects, assessed with 2 different scales (3 subscores ...
0
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0answers
37 views

SPSS Contrasts for a Five-Way Within-Subjects ANOVA (Yes, You read correctly)

I have a 4 x 4 x 2 x 2 x 2 repeated measures design and I'm trying to test a contrast for just the first variable (here called "SOA"), averaging over the others, in SPSS. Initially, I thought it ...
1
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0answers
71 views

Linear trend in SAS using contrast

I've been struggling with this problem for a couple of hours, and I could use some advice. I have a linear regression model with two continuous predictors and a categorical one (with 4 levels). I ...
1
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1answer
50 views

Orthogonal contrasts for four levels - are Helmert contrasts orthogonal?

I am planning to do a 2-way mixed ANOVA with the within-subjects factor having four levels. Since the exact data do not matter, I hope to suffice by only providing a general question. On my ...
3
votes
1answer
92 views

Design of matrix of contrasts in R

I am doing some post-hoc comparisons (in lme4, but here I'll just present a simple linear model), and I am having a hard time making sure that I am building the right matrix of contrasts to test ...
1
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0answers
24 views

Specific contrasts in mixed model with interaction

I have a dataset consisting of two groups tested across three days. Therefore I run a linear mixed model as follows: ...
2
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0answers
125 views

R model.matrix and makeContrast. Understanding model and possible contrast

I have measurements from 12 mice, grouped in two conditions. I each mouse I have measurements from 4 tissues. The design is not balanced, 5 mice in condition1 and 7 in condition2. After reading the ...
1
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0answers
37 views

Logistic regression: Trying to use mean logit as reference group

Question I would like to do a logistic regression where the independent variables are compared to the mean logit, rather than the logit being compared a certain reference group. Example The example ...
1
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0answers
30 views

combining and contrasting time course GLMs using R

I am analyzing some time course data in which I have set up a GLM using R for each subject. Each GLM I want to run is an attempt to extract estimates of different behavioral conditions effects on the ...
0
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0answers
54 views

R lm without intercept strange contrast

I am actually doing a linear regression without intercept lm(y~ -1 + a + b + c + d ), where b, ...
0
votes
0answers
19 views

counfounded batch effects in microarray dataset - can I do partial experiment redesign?

I'm working with a microarray data set where the batches are completely confounded treatment time, i.e. time t1 is all in batches b1 and b2, and time t2 is all in batches b3, b4, and b5. I know this ...
0
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0answers
24 views

Testing linear contrast in an unbalanced longitudinal design (R)

I'm experiencing some conceptual problems in testing a linear contrast in an unbalanced longitudinal design. I have performed some correlation analysis with brain imaging data. These analysis ...
2
votes
1answer
107 views

Polynomial contrasts for regression

I cannot understand the usage of polynomial contrasts in regression fitting. In particular, I am referring to an encoding used by R in order to express an interval ...
1
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0answers
30 views

Can one perform trend analysis with ANOVA?

I'm using the multcomp package in R to do a trend test as part of an ANOVA. I am wondering if it is possible to not only ask "is there a trend" within one of the treatments but also "are the trends ...
2
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0answers
44 views

How to reconcile SAS hazard ratio standard error with actual value

I am trying to replicate the "C3 Contrast" (Output 66.3.7) at the bottom of: http://support.sas.com/documentation/cdl/en/statug/63962/HTML/default/viewer.htm#statug_phreg_sect048.htm I am able to ...
1
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0answers
36 views

How to perform a constrast in R for a cox proportional hazards model

I have the following model fit: ...
1
vote
1answer
41 views

Non-omnibus ANOVA test

Let's say I have $N$ groups that are mutually independent ($X_1,\ldots,X_N$). What I am looking for is a p-value to test the null hypothesis "$\mu_1=\mu_2\vee\mu_1=\mu_3\vee\ldots\vee\mu_1=\mu_N$", if ...
0
votes
1answer
105 views

Tests of within subjects contrasts in R

I have run a split splot model in SPSS (via repeated measures function) and I would like to reproduce my results using R. To do so I used ezANOVA function from ez package to obtain sphericity tests ...
1
vote
0answers
20 views

Testing contrast between low/high and high/low

I'm trying to understand the results published in Sagristano, Trope, and Liberman (2002). Specifically, I don't understand what analysis produced the result highlighted in the screenshot below. The ...
1
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0answers
43 views
0
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2answers
32 views

How to code and interpret a regression with 4-level categorical variable and continuous covariates

I have a problem in which 4 groups of people are compared in their performance on a certain test. One way anova shows that they are in fact different. But I also know that my groups are different in ...
4
votes
1answer
90 views

What is a “contrast” in a Principal Component Analysis (PCA)?

I have been studying how to interpret principal components. I recently came across an example of a particular eigenvector: $$e_j^T = \left[ \frac{\sqrt{2} }{2}, \frac{-\sqrt{2} }{2}, 0, \dots,0 ...
2
votes
1answer
149 views

How to define weights when testing an exponential trend?

In a linear model including ANOVA one can test a trend (e.g., linearity, quadratic effect, etc.) among the ordered effects (regression coefficients or factor levels) through assigning proper weights. ...
3
votes
0answers
64 views

How to run a power analysis for a repeated measures (all within-subjects) with combined contrasts?

I am looking for a little help on determining the correct way to run a power analysis on a within-subjects repeated measures design (i.e., no between subjects variable) with combined contrasts. ...
0
votes
0answers
72 views

Repeated measures logistic regression

I have a dataset that features a binary outcome, a binary predictor, and an unordered factor with 7 levels, and 120 subjects. Each of the 120 subjects were asked a binary question on seven issues, ...
0
votes
0answers
15 views

Testing batch differences in GWAS

I have some genotyping (~half a million response variables) data that was run in 4 batches (190 total samples, spread over 4 batches). The samples are from a case-control study (95 cases, 95 ...
0
votes
0answers
53 views

What happens with covariates when doing contrasts?

I am doing an analysis of covariance (in SPSS) but can't find anywhere how does SPSS treat the covariates when producing the analysis for the special contrasts I specified. Does it take them at their ...
1
vote
1answer
126 views

Contrasts with interactions

I have a couple of questions about contrasts but would also appreciate any suggestions for relevant literature. I am carrying out a GLM (binomial). There are 3 Factors (A,B,C) - A has 3 levels, B ...
0
votes
0answers
74 views

SPSS/Stata Repeated Measures - Contrast question

I have data from 8 subjects collected at 5 time points. I would like to see if there is a difference between time points (1 + 2) and (3 + 4 + 5) using either SPSS or Stata. When in SPSS I use ...
0
votes
0answers
70 views

What is the default contrast coding for the interaction test in a 3x2 ANOVA?

As far as I understand it, the interaction term in a traditional 2x2 ANOVA is great for detecting a disordinal interaction, because the test assumes that the interaction is of form (-2, -2, 2, 2) ...
0
votes
2answers
295 views

Contrast to test significant interaction - why not include main effect?

Given a data set with a continuous outcome variable $Y$ and two nominal IV $X_1$ and $X_2$ which have 4 (A,B,C,D) and 3 (E,F,G) levels respectively, we can assign the first level of each as a ...
0
votes
1answer
533 views

Specifying contrasts for lme in 3x3 repeated-measures design

I would like to test the effects of two categorical variables, each with 3 levels, on some continuous data. Three groups of participants completed the same task for 3 types of stimuli, so it's a 3x3 ...
4
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0answers
271 views

Contrast matrix definition

What exactly is contrast matrix and how exactly is contrast matrix specified? I.e. what are columns, what are rows, what are the constraints on that matrix and what does number in column ...
4
votes
0answers
113 views

Interpretation of intercept in Helmert coding

I have a general, presumably simple, question, but I couldn't find a conclusive answer so far. Assume I have a simple case of a General Linear Model with one categorical predictor variable, that has ...
0
votes
0answers
74 views

Contrasts for one factor in a repeated-measures ANOVA

I am trying to set custom orthogonal contrasts for a repeated-measures design using R. Is it possible to set contrasts just for one factor? The model looks like this: ...
4
votes
1answer
150 views

GLMM model specification help gender effects + an effect that is nested only within female

Main question: "What are the contributing variates to daily movement distances?" Specifically my question today relates to: "What is the contribution related to gender, and then within female what ...
6
votes
1answer
76 views

Looking for the 'Elbow' in data

Subitization is the rapid, accurate enumeration of low-numerosity displays, distinguished from counting by a sharp non-linearity in the plot of response times. Below is a representative plot, from ...
2
votes
0answers
44 views

One factor repeated measures where first time point is a control

Patients were randomized to two groups (control and intervention). Each patient is evaluated at 3 time points. The first time point is taken pre-intervention, so it should have the same mean response ...
1
vote
1answer
180 views

Non-Orthogonal Planned Comparison: How to correct for alpha?

I have a data set containing three groups (A, B, C). Group A and Group B have undergone two different types of training designed to improve the same thing. Group C is my control group with no ...
2
votes
1answer
159 views

Inverse matrix for contrast coding

I'm trying to understand how "user defined contrast coding" works. My question refers to the example from http://www.ats.ucla.edu/stat/r/library/contrast_coding.htm#User: ...
2
votes
0answers
69 views

User-defined contrast on Generalized Estimating Equations

I am running a GEE on SPSS as well as Stata on choice data with the following structure: Each subject completed 32 trials in 4 ...
4
votes
0answers
94 views

Computation of polynomial contrast variables

Please give me idea how to efficiently recode a categorical variable (factor) into the set of orthogonal polynomial contrast variables. For many types of contrast variables (e.g. deviation, simple, ...
8
votes
0answers
110 views

Testing certain contrasts: Is this provably a hard problem, or not?

I posted this to mathoverflow and no one's answering: Scheffé's method for identifying statistically significant contrasts is widely known. A contrast among the means $\mu_i$, $i=1,\ldots,r$ of $r$ ...
2
votes
2answers
302 views

Defining contrasts in ANOVA to compare mean differences

I would like to run an analysis of variance (parametric or not) with two factors; each factor having two levels. So if x, y is are the levels of the first factor and 1, 2 the levels of the second I ...