Many thanks for your explanation! have a nice weekend! JP- --On Friday, February 17, 2006 3:11 PM -0500 "James W. MacDonald" <jmacdon at="" med.umich.edu=""> wrote: > Hi Jianping, > > Jianping Jin wrote: >> Thanks James! >> >> Please forgive my ignorance if I am wrong. I knew "fit$coefficients" >> stuff. That just give me "coefficients". Is that "b" in y = a + bx? It >> must be more complicated than that I guess. In my case I just used >> default "design" in fitting as below: > > Well, that formula is conventionally used to describe a linear regression > where there is some concept of slope. We are fitting an ANOVA model, and > since there is no ordering of the factor levels, there is no concept of > slope. A more conventional formula for ANOVA (without the subscripts) > would be something like > > y = a + b + error > > The coefficients would correspond to 'a' and 'b', which depending on the > design matrix can mean different things. > >> >> fitR <- lmFit(RG$R, ndups=2, spacing=722, correlation=0.5205939) > > Hmmm. I haven't done any cDNA work in years, but I don't think that looks > right. If I am not mistaken, what you are doing is fitting a one- sample > t-test on just the cy5 (or is cy3 red? I can never remember) values which > is usually not what you want. The convention is to fit a one-sample > t-test on the log ratios, which then tests to see if the average log > ratio is different from zero (which corresponds to testing if the average > fold change is different from one). > > The model here would be > > y = a + error > > >> >> What if I am interested in getting all "y" values for each gene in each >> chip after lmFit fitting? Do I need to calculate them out following some >> formula? Or I can extract them from somewhere within the limma package? > > If by 'y' values you mean the fitted values, you would get those from the > fit$coefficients, which in your case should just be a vector, one value > per gene. > > HTH, > > Jim > > > >> >> Thanks again! >> >> Jianping >> >> --On Friday, February 17, 2006 1:27 PM -0500 "James W. MacDonald" >> <jmacdon at="" med.umich.edu=""> wrote: >> >> >>> Jianping Jin wrote: >>> >>>> Dear list, >>>> >>>> Could anyone point me out how to extract the results from lmFit? The >>>> on-line document said "the probe-wise fitted model results are stored >>>> in a compact form". What I wanted to get is ALL data values after >>>> linear model normalization instead of going through all limma >>>> processes. >>> >>> The results are output in a named list. As with all named lists, you can >>> extract the names using names(listname). If, for example, your lmFit() >>> output is called 'fit', you can get information in several ways: >>> >>> names(fit) ## gives names >>> fit ## outputs first 10 or so values in each list component >>> fit$coefficients ##extract coefficients >>> fit$p.value ## p-values >>> etc. >>> >>> See ?list, ?"[[" for more information. >>> >>> HTH, >>> >>> Jim >>> >>> >>> >>>> Thanks in advance! >>>> >>>> Jianping >>>> >>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >>>> x Jianping Jin Ph.D. x >>>> x Bioinformatics scientist x >>>> x Center for bioinformatics x >>>> x 3133 Bioinformatics Building x >>>> x CB# 7104 x >>>> x University of North Carolina x >>>> x Chapel Hill, NC 27599 x >>>> x Tel: (919)843-6105 x >>>> x Fax: (919)843-3103 x >>>> x E-mail: jjin at email.unc.edu x >>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Affymetrix and cDNA Microarray Core >>> University of Michigan Cancer Center >>> 1500 E. Medical Center Drive >>> 7410 CCGC >>> Ann Arbor MI 48109 >>> 734-647-5623 >> >> >> >> >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> x Jianping Jin Ph.D. x >> x Bioinformatics scientist x >> x Center for bioinformatics x >> x 3133 Bioinformatics Building x >> x CB# 7104 x >> x University of North Carolina x >> x Chapel Hill, NC 27599 x >> x Tel: (919)843-6105 x >> x Fax: (919)843-3103 x >> x E-mail: jjin at email.unc.edu x >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Jianping Jin Ph.D. x x Bioinformatics scientist x x Center for bioinformatics x x 3133 Bioinformatics Building x x CB# 7104 x x University of North Carolina x x Chapel Hill, NC 27599 x x Tel: (919)843-6105 x x Fax: (919)843-3103 x x E-mail: jjin at email.unc.edu x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx