User: De-Jian ZHAO

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De-Jian ZHAO240
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Posts by De-Jian ZHAO

<prev • 24 results • page 1 of 3 • next >
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Comment: C: R/Maanova Tutorial
... Thank you for your responses, Ricardo and Juan Pedro. You have proposed some evidence for the alphabetical order, but I think they are not direct proofs. I am thinking this question may be solved by reading the source codes of the functions. The fitting to the model occurs in the function fitannov ...
written 9.1 years ago by De-Jian ZHAO240
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Answer: A: R/Maanova Tutorial
... Thank you for your detailed tutorial, Ricardo. It is a great help to me, but there is still something confusing me. It is about the contrast matrix. Simply speaking, I don't know how to decide the meanings of the columns in the contrast matrix. You ASSUME the experimental groups are stored alphabe ...
written 9.1 years ago by De-Jian ZHAO240
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Comment: C: about formula in ancova
... How can we easily find out the kind of sums of squares produced by some package and function? It seems that it is not easy to switch from one kind to another. Thanks. Dejian Juan Pedro Steibel wrote: > Good morning, > I'd add that given an object of class lm in R, there is a package > ca ...
written 9.1 years ago by De-Jian ZHAO240
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Answer: A: about formula in ancova
... Thank you for your explanation, Richard. But I want to confirm whether I understand you correctly. Take "ancova(Sodium ~ Calories + Type, data=hotdog)" for example. Calories is the covariate in the formula, right ? If Calories is the covariate, the result of that command shows Type is significant ( ...
written 9.1 years ago by De-Jian ZHAO240
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Answer: A: about formula in ancova
... To provide more details about the confusing results mentioned in my previous email. Some parameters (eg. Sum Sq, Mean Sq, F value, Pr) about the two variables seem to depend on the order in the formula, and the variation of probability (Pr) directly changes the significance. As to my own data, chang ...
written 9.1 years ago by De-Jian ZHAO240
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about formula in ancova
... Dear list members, I have a question about the formula in ancova(), which is embedded in the HH package.There are several examples in the ancova() help file which can be accessed by type "?ancova" in R console after loading HH package.Some codes are as follows: hotdog <- read.table(hh("dataset ...
written 9.1 years ago by De-Jian ZHAO240
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Answer: A: Different expression direction between limma microarray data analysis vs quantit
... Have you ever checked the original microarray images? Sometimes some badly-printed spots may pass the QC and lead to this kind of weired problems. Chances are higher if you have less replicates. I'm just fancying.... jixinwang at tamu.edu wrote: > Dear all, > > I use limma package to do m ...
written 9.6 years ago by De-Jian ZHAO240
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dye effect in limma
... Hi, I have a question about evaluating dye effects in limma. In chapter 8.1.2 of limma users guide, an example is given to demonstrate how to estimate dye effects. The design matrix is constructed by the following command: >design <- cbind(DyeEffect=1,MUvsWT=c(1,-1,1,-1)) > design ...
limma written 9.9 years ago by De-Jian ZHAO240
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Comment: C: Does factDesign deal with two-color data?
... Many thanks for your responses. The package can deal with two-color data according to Robert. I get the answer. Thanks to Denise and Alberto for suggestions. Alberto Goldoni wrote: > Hi Dejian, > > for this array data i have used RankProd package that is based on the rank > product meth ...
written 9.9 years ago by De-Jian ZHAO240
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Does factDesign deal with two-color data?
... Hi, I learned about factDesign package from a scientific article which deals with affy data. The command library(help=factDesign) invokes some information about this package. It shows that this package "Suggests: affy". Therefore I wonder whether the factDesign package can deal with two-color ...
microarray genefilter affy factdesign written 9.9 years ago by De-Jian ZHAO240 • updated 9.9 years ago by Denise Scholtens70

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