[BioC] duplicate correlation of 4 "within array replicates" limmaGUI

[Christine Voellenkle]

Dear Gordon,
Excuse me for the last mail, I simply replied, I didn't realise that I was
sending it to your personal email.

Thank you a lot for your fast answer!
I attached a schema of the slide-design, also with an example of the 4
replicates, hoping that like this I could explain it sufficiently.
For my understanding the replicates are regularly arranged.
As example mir 16, which we use as control mir, its 4 replicates can be
found in block 5, block 13, block 21 and block 29, always with the same
coordinates: column 9, row 3.
If I count along the column there are 21 spots between the replicates (NOT
counting the replicates), if I count along rows there are 127 spots between
the replicates, but also this leads to an error message.
I could not imagine another way to count the distance.
I followed your advice, to see if limma tells me the distance using the
comand getLayout, but as spacing he tells me not available/missing value

$ngrid.r
[1] 8
$ngrid.c
[1] 4
$nspot.r
[1] 11
$nspot.c
[1] 16
$ndups
[1] 4
$spacing
[1] NA
attr(,"class")
[1] "PrintLayout"
>

I wondered, since limma recognizes the 4 replicates
$ndups
[1] 4
if it is enough to tell him spacing 1, I tried it, but it doesn't work, in
the top table list gives a weired result, there are mir missing and  it's
shrinking the 4 replictes into 2 for every mir.

What would you advice?
Thanks a lot, Christine

-- 
Dr. Christine Völlenkle, Ph.D.
Research Laboratories-Molecular Cardiology
I.R.C.C.S. Policlinico San Donato
Via R. Morandi, 30
20097  S. Donato M.se (MI) Italy
Phone: +39 02 52774 683 (lab)
          +39 02 52774 533 (office)
Fax:    +39 02 52774 666
email: christine.voellenkle at gmail.com