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Dear list, I have a microarray data in which gene expression is the response (dependent) variable. Can anybody tell me which package/function in R should I use to model the gene expression with an ordinal predictor (Independent Variable) Thanks...

Dear Douglas and R-help, Does lme assume normal distribution AND equal variance among groups like anova() does? If it does, is there any method like unequal variance T-test (Welch T) in lme when each group has unequal variance...

Dear R help, In limma package, contrasts.fit() function is very useful. I am wondering whether there is a similar function for lme object, which means given a mixed linear model fit, compute estimated coefficients and standard errors for a...

Dear list, In terms of dbSNP database in NCBI, I can get the chr_rpts files for the most recent 37.3 assembly from the following FTP site, ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/ My...

Dear R-help, In nlme package, anova () can be used to test the difference between two coefficients as shown on page 225 of "Mixed Effects Models in S and S-Plus": anova(fm2BW.lme, L = c("Time:Diet2" = 1, "Time...

Hi, There are 20 subjects grouped by Gender, each subject has 2 tissues (normal vs. cancer). In fact, it is a 2-way anova (factors: Gender and tissue) with tissue nested in subject. I've tried the following: Model 1...

I'm working with a nested model (mixed). I have four factors: Patients, Tissue, sex, and tissue_stage. Totally I have 10 patients, for each patient, there are 2 tissues (Cancer vs. Normal). I think Tissue and sex are fixed...

Dear Dr. Bates, and R-help, I've tried the anova function to test the difference between two coefficients, as shown on page 225 of your book "Mixed Effects Models in S and S-Plus (Statistics and Computing)". When I...

Dear Dr. Bates, and R-help, I just found the reason I got the error message is because I copied the code directly from the book. When I tried the code in "~\library\nlme\scripts" under the R installation directory...

Thanks for Spencer and Simon's help. I've got very interesting results based on your suggestions. One more question, how to handle unequal variance problme in lm()? Isn't the weights option also, which means weighted least squares, right...

Hi Simon, Thanks for your reply. Your reply reminds me that book. I've read it long time ago, but haven't try the weights option in my projects yet:) Is the heteroscedastic test always less powerful because we have...

Hi Max, Thanks for your prompt reply. Actually I have already checked contrast package, but I still could not figure out how to set the contrast matrix for a 2x2 factorial design. I would like to set a contrast exactly...