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2answers
51 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
21 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
21 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
32 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
42 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
39 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
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1answer
73 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
73 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
35 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
27 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
49 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
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0answers
15 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 ...
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0answers
22 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
80 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
votes
0answers
40 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
35 views

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

I have the following model fit: ...
1
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1answer
40 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
87 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
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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
41 views
0
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2answers
29 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
89 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
133 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
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0answers
55 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
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0answers
67 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, ...
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0answers
14 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
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0answers
52 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
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1answer
120 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
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0answers
71 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
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0answers
59 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
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2answers
281 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
474 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
195 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
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0answers
106 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
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0answers
66 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
149 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
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1answer
72 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 ...
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0answers
43 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
155 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
153 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
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0answers
66 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
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0answers
90 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, ...
7
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0answers
106 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
272 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 ...
2
votes
0answers
81 views

A contrast suggested by the data

One approach to testing hypotheses suggested by the data is Scheffé's method. According to the Wikipedia article, the contrast $C = \sum_{i=1}^r c_i \mu_i$ (where $\sum_{i=1}^r c_i=0$) is estimated ...
1
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0answers
83 views

How to Partition An Interaction SS in ANOVA

I'm a new user of R and I'm trying to replicate Table 6.18 on page 262 in Statistical Procedures in Agricultural Research, By K. A. Gomez and A. A. Gomez. New York, Chichester, etc.: Wiley (1984). ...
0
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0answers
87 views

How to avoid regression to the mean in a simple comparison

This is a pretty simple question but I haven't been able to find a clear answer to it. I have some data from a behavioral experiment taken under two conditions (A and B); within each condition, each ...
2
votes
2answers
1k views

Plotting predicted values in GLM in R

I am trying to find a more aesthetic way to present an interaction with a quadratic term in a logistic regression (categorisation of continuous variable is not appropriate). For a simpler example I ...