## User: De-Jian ZHAO

De-Jian ZHAO •

**240**- Reputation:
**240**- Status:
- Trusted
- Location:
- Last seen:
- 9 years, 1 month ago
- Joined:
- 12 years, 2 months ago
- Email:
- z*****@ioz.ac.cn

#### Posts by De-Jian ZHAO

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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 ZHAO •

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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 ZHAO •

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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 ZHAO •

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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 ZHAO •

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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 ZHAO •

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... 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 ZHAO •

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... 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 ZHAO •

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... 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
...

written 9.9 years ago by
De-Jian ZHAO •

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... 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 ZHAO •

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... 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 ...

written 9.9 years ago by
De-Jian ZHAO •

**240**• updated 9.9 years ago by Denise Scholtens •**70**#### Latest awards to De-Jian ZHAO

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