Dear Gordon,
the spacing 1408 worked, perfectly!!! Thank you so much!
Christine

On Wed, Oct 15, 2008 at 3:34 AM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> 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
> 8*32=1408.
>
> 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
> Gordon
>
>
> ----------- 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 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 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
>



-- 
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@gmail.com

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