[BioC] asMatrixWeights: weights of unexpected shape

[Gordon K Smyth]

Dear Christine,

This error should never occur in limmaGUI, so I am forwarding this email 
to the limmaGUI maintainer, Keith Satterley.

I do wonder why you are inputting the GAL file at all, since it is not 
required.  The same information is in the gpr files.

Best wishes
Gordon

> Date: Tue, 14 Oct 2008 10:55:06 +0200
> From: "Christine Voellenkle" <christine.voellenkle at gmail.com>
> Subject: [BioC] asMatrixWeights (weights, dim(M)),	weigths of
> 	unexpected shape
> To: bioconductor at stat.math.ethz.ch
>
> 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 at gmail.com