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

Gordon K Smyth smyth at wehi.EDU.AU
Wed Oct 15 03:34:53 CEST 2008

Dear Christine,

If your arrays truly consist of four subarrays, with each subarray having 
identical probes in the same arrangement, then the spacing between 
duplicates is 1/4 of the total number of spots, i.e.,

    spacing <- nrow(MA)/4

According to your previous email, your data has 5632 rows, so the spacing 
is 5632/4=1408.  Note that each of your meta blocks has 32 spots, so the 
spacing represents the eight metablocks making up one subarray, that is 

The limma documention tells you that spacing represents the number of rows 
in the data object or GAL file separating the replicate arrays.  This is 
not the same as the number of rows or columns which you count in a 
straight line on the image, as you seem to be assuming.

I'm sorry that getLayout() didn't correctly deduce the spacing for you. 
The function was written mainly with ndups=2 in mind.

Best wishes

----------- original message ---------------
[BioC] duplicate correlation of 4 "within array replicates" limmaGUI
Christine Voellenkle christine.voellenkle at gmail.com
Tue Oct 14 11:04:29 CEST 2008

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 
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

[1] 8
[1] 4
[1] 11
[1] 16
[1] 4
[1] NA
[1] "PrintLayout"

I wondered, since limma recognizes the 4 replicates
[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 Vllenkle, 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

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