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TEXTORIS Julien
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@textoris-julien-1412
Last seen 10.3 years ago
Dear all,
First thing, happy new year to all and thanks for all the
knowledge/advices brought through the list !
I would like to have your advice/comments on the following design.
I have to analyse a microarray dataset performed on MoGene ST 1.0
which
comprise 22 arrays. I have allmost no replicates (! could not control
this !) but I thought I could use the timecourse and double KO/single
KO
status to overcome this ?
The variables are :
- Treatment : binary YES or NO
- Time : samples at 0h (= UNTREATED), 2h, 6h and 18h
- Strain : Wild type (WT), single KO for gene A or gene B, and
double KO.
For WT mice, I have 2 UNTREATED (=0h), and a timecourse for Treatment
1
and 0 (WT_UNT_2h, and WT_TTT_2h). For KO mice, I only have treated
samples (except time 0h, which is considered untreated).
I have duplicates only for WT.UNTREATED_0h and KOA_0h.
I wrote the following design :
levels(f) =
c("WT_0h","WT_2h","WT_6h","WT_18h","WT_UNT_2h","WT_UNT_6h","WT_UNT_18h
","KOA_0h","KOA_2h",
...,"DKO_0h","DKO_2h","DKO_6h","DKO_18h")
and performed the contrast matrix over time like his :
cont.wt = contrast.matrix(
"WT_18h-WT_6h",
"WT_6h-WT_2h",
"WT_2h-WT_0h",
levels=design)
idem for KOA, KOB and DKO, and then the comparisons :
cont.koa.wt = contrast.matrix(
"(KOA_18h-KOA_6h)-(WT_18h-WT_6h)",
etc...
How would you handle the strain variable ? As one variable with four
levels : WT, KOA, KOB, DKO ? Or is it possible to take into account
that
DKO is somehow like KOA+KOB ? Do I have to transform 'Strain' into
three
binary variables : WT (1/0), KOA(1/0) and KOB (1/0) and code DKO as
KOA
= 1 and KOB = 1 ?
The second question is I don't know how to integrate the WT mice that
are untreated ?
This experimental design is a bit too complex for me, so any advice
would be greatly appreciated !
Thanks in advance,
Julien