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

I have also another problem with limma GUI- the Gene pix flag weighting.
In my gpr file I have flag bad (-100), flag not found(-50) and unflagged
(0), when I use spot quality weighting and some steps later I choose only 2
of the spot types (mir and mirPlus) I get the error message:
"asMatrixWeights (weights, dim(M)), weigths of unexpected shape"
I checked the mailing list and saw that you recommended someone else witht
the same problem to check the size of the objects.
I tried to do this inserting in the R console "dim(weights)" immedialtely
after choosing the spot qualities in the limma Gui and it tells  "NULL",
which doesn't look fine to me. But I'm not sure if performing the setting of
the flags on the GuInterface creates an object "weight" in R console?
Since I am using limma GUI, I do not understand where I am introducing the
error, since the only information I give is the gal and gpr file- they
contain the same number of features. The sum of the spottypes that he is
reading from the spottype file is correct (corresponds to the number of
features in gal and gpr file,= 5632)

Read CV 40_900750_110908.gpr
Read CV41_complete1_900740_120908.gpr
Read CV42_complete1_900760_120908.gpr
Read CV43_upsidedown1_9000740_250908.gpr
Read CV44_complete1_900750_300908.gpr
Matching patterns for: ID Name
Found 2904 mir
Found 152 miRPlus
Found 8 positivectrl
Found 40 positivectrl2
Found 28 negativectrl
Found 316 spikes
Found 156 virus
Found 68 virus1
Found 8 virus2
Found 12 virus3
Found 68 virus4
Found 8 virus5
Found 1616 noname
Found 88 empty
Found 160 Hy3
Setting attributes: values Color
> weights (dim)
NULL

If something is wrong with the dimensions of the object I load I guess this
could also explain the problems that I have with the replictaes?
THank you very much for your time and your support,
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@gmail.com

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