asMatrixWeights: weights of unexpected shape
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@gordon-smyth
Last seen 24 minutes ago
WEHI, Melbourne, Australia
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 V?llenkle, 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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@christine-voellenkle-3067
Last seen 7.1 years ago
Dear Gordon, I tried it without inputting also the GAL file- and it worked, thank you so much!!! Grazie mille! Even if there shoudn't be a contradiction between gpr and gal information, bvecause I created the gpr using exactly this gal file. Greetings Christine On Wed, Oct 15, 2008 at 3:41 AM, Gordon K Smyth <smyth@wehi.edu.au> wrote: > 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@gmail.com> >> Subject: [BioC] asMatrixWeights (weights, dim(M)), weigths of >> unexpected shape >> To: bioconductor@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@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 [[alternative HTML version deleted]]
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