[BioC] normalizeBetweenArrays gives an error

[Michael Nuhn]

Hello Gordon!

> First of all, an incidental but important point.  The subject of your
email says
> "normalizeBetweenArrays gives an error" but this is not true.  Your error
came when you tried to
> convert an marrayNorm object into an MAList object.  You never got to the
point of using
> normalizeBetweenArrays.  You would have a better chance of getting help
from the right people if
> your email subject said "converting marrayNorm to MAList gives an error"
or similar.

Yeah, that was not very smart.

> The purpose of the maSub slot is to record incomplete gpr files.  The fact
that maSub has length
> 7000 with 6912 TRUE values means that the number of print-tip groups on
your arrays implies 7000
> spots but actually 88 of these spots are omitted from your gpr files,
probably because they are
> "empty" or "blank" spots.  Since you are in a Bioinformatics group, you're
probably a computer
> savvy person, so you can probably confirm easily that your gpr files
contain only 6912 data rows.

Ah, ok, thanks for that.

I will ask the biologist who designed the array about the empty spots but I
guess thats the reason for my problem.

And as the computer savvy person I am, I have checked the GPR file and there
are indeed only 6912 data rows.

> In your case, you have already completed print-tip loess normalization on
your data object.  So
> you no longer have any need to keep track of which spots are from which
print-tip group.  So you
> could simply set maSub(gn) <- TRUE without any problems.

Done.

Thanks for your help Gordon and greetings from Germany,
Michael.

--
-----------------------------------------------------------
Dipl.-Inform. Michael Nuhn
Bioinformatik
Zentrum für Nanostrukturtechnologie und
Molekularbiologische Technologie

+49 (0)631 - 205 4334
nuhn at rhrk.uni-kl.de
http://nbc3.biologie.uni-kl.de/