From: Assa Yeroslaviz <frymor_at_gmail.com>

Date: Thu 16 Feb 2006 - 23:12:34 EST

attr(,"assign")

[1] 0 1 2 3

attr(,"contrasts")

attr(,"contrasts")$"factor(estrogen)"

[1] "contr.treatment"

attr(,"contrasts")$"factor(time.h)"

[1] "contr.treatment"

Date: Thu 16 Feb 2006 - 23:12:34 EST

Hi,

at the moment I'm trying to understand the limma/affy Packages. I've tried
every example I could find to try and understand the ways to create design
and contrast matrices. I must admit though, that I can't figure it out. I
did a few times the estrogen files from the book "bioinformatics and
computational biology solutions using R and Bioconductor".
I know it's a difficult question to answer, but I need all the help I can
get.

1. how does one suppose to build the design matrix by knowing what one wants
to examine? this is the created matrix in the book:

Intercept ES T48 ES:T48 low10-1.cel 1 0 0 0 low10-2.cel 1 0 0 0 high10-1.cel 1 1 0 0 high10-2.cel 1 1 0 0 low48-1.cel 1 0 1 0 low48-2.cel 1 0 1 0 high48-1.cel 1 1 1 1 high48-2.cel 1 1 1 1

attr(,"assign")

[1] 0 1 2 3

attr(,"contrasts")

attr(,"contrasts")$"factor(estrogen)"

[1] "contr.treatment"

attr(,"contrasts")$"factor(time.h)"

[1] "contr.treatment"

2. There are some design matrices where the first column is full of '1' (intercept). What does it mean? can I do without this column?

3. How do I create the contrast matrix if I want to examine the differences
in the gene expression between 10 hours and 48 hours?
ES - with estrogen in 10 hours

T48 - time 48 hours

ES:TS - probes with estrogen and in 48 hours

(Just by the way:

4. does everything has to do with matrices multiplications? )

the book propose this contrast matrix:

> contM <- cbind(es10=c(0,1,0,0), es48=c(0,1,0,1)) > contM

es10 es48

*[1,] 0 0
*

[2,] 1 1

*[3,] 0 0
**[4,] 0 1
*

5. But why? How do I suppose to know it? Is it also a multiplication of some
matrices?

6. What stands the columns or the lines for?

I'll be happy for every kind of help I can get. If someone know where I can read about it, it would be also of great need.

**THX,
**
Assa

-- Assa Yeroslaviz Loetzener Str. 15 51373 Leverkusen [[alternative HTML version deleted]] ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.htmlReceived on Thu Feb 16 23:19:09 2006

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