Question

LimmaGUI spot type files

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Elizabeth Brooke-Powell ▴ 160

@elizabeth-brooke-powell-838

Last seen 9.7 years ago

Hi there, I was wondering if someone might be able to answer what I hope is a very simple question about LimmaGUI's spot type files. Do you have to type the full name in the file or can you use partial names with an asterisk? For example all of my gene IDs always start with TgEST followed by various numbers, can I type TgEST* to identify all genes and then * for all controls? All of my controls have different sorts of names. Do I have to copy each of the names into the table and label them as controls? Thank you for any help you can give, Liz Molteno Building Department of Pathology University of Cambridge Tennis Court Road Cambridge, CB2 1QP United Kingdom Website: http://www.path.cam.ac.uk/~toxo/ Tel 01223 33 33 31(office) or 01223 33 33 29 (lab) [[alternative HTML version deleted]]

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ADD COMMENT • link updated 19.8 years ago by Gordon Smyth 50k • written 19.8 years ago by Elizabeth Brooke-Powell ▴ 160

score 0 · Answer 1 · 2004-07-27

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Gordon Smyth 50k

@gordon-smyth

Last seen 2 minutes ago

WEHI, Melbourne, Australia

At 09:42 PM 26/07/2004, Elizabeth Brooke-Powell wrote: >Hi there, > >I was wondering if someone might be able to answer what I hope is a very >simple question about LimmaGUI's spot type files. >Do you have to type the full name in the file or can you use partial names >with an asterisk? For example all of my gene IDs always start with TgEST >followed by various numbers, can I type TgEST* to identify all genes and >then * for all controls? All of my controls have different sorts of names. Yes, this will work. However you must put the * for controls before the TgEST* line in your spot types file. Gordon >Do I have to copy each of the names into the table and label them as >controls? > >Thank you for any help you can give, > >Liz > >Molteno Building >Department of Pathology >University of Cambridge >Tennis Court Road >Cambridge, CB2 1QP >United Kingdom > >Website: http://www.path.cam.ac.uk/~toxo/ >Tel 01223 33 33 31(office) or 01223 33 33 29 (lab)

ADD COMMENT • link 19.8 years ago Gordon Smyth 50k

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Hi, If you're having trouble with spot types, one other thing I might point out is that each spot type in the SpotType column is supposed to be unique, e.g. RatioControl1, RatioControl2, whereas in the ID or Name column (or whatever columns you use), you can have the same pattern e.g. Scorecard* in more than one row of the SpotTypes table. Regards, James

ADD REPLY • link 19.8 years ago James Wettenhall ▴ 1000

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Gordon, Just one point of clarification, do you mean the order of spot types must be like this: SpotType ID Name Color Control * * orange Est TgEST* * black Vector Bluescript* * yellow Empty * unknown red Water * Water blue As opposed to this: SpotType ID Name Color Est TgEST* * black Vector Bluescript* * yellow Empty * unknown red Water * Water blue Control * * orange Thank you for your help, Liz -----Original Message----- From: Gordon Smyth [mailto:smyth@wehi.edu.au] Sent: 27 July 2004 08:07 To: Elizabeth Brooke-Powell Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] LimmaGUI spot type files At 09:42 PM 26/07/2004, Elizabeth Brooke-Powell wrote: >Hi there, > >I was wondering if someone might be able to answer what I hope is a very >simple question about LimmaGUI's spot type files. >Do you have to type the full name in the file or can you use partial names >with an asterisk? For example all of my gene IDs always start with TgEST >followed by various numbers, can I type TgEST* to identify all genes and >then * for all controls? All of my controls have different sorts of names. Yes, this will work. However you must put the * for controls before the TgEST* line in your spot types file. Gordon [[alternative HTML version deleted]]

ADD REPLY • link 19.8 years ago Elizabeth Brooke-Powell ▴ 160

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At 05:40 PM 27/07/2004, Elizabeth Brooke-Powell wrote: >Gordon, > >Just one point of clarification, do you mean the order of spot types must >be like this: > >SpotType >ID >Name >Color >Control >* >* >orange >Est >TgEST* >* >black >Vector >Bluescript* >* >yellow >Empty >* >unknown >red >Water >* >Water >blue > >As opposed to this: > > >SpotType >ID >Name >Color >Est >TgEST* >* >black >Vector >Bluescript* >* >yellow >Empty >* >unknown >red >Water >* >Water >blue >Control >* >* >orange Yes. More general must go first. Gordon >Thank you for your help, > >Liz > >-----Original Message----- >From: Gordon Smyth [mailto:smyth@wehi.edu.au] >Sent: 27 July 2004 08:07 >To: Elizabeth Brooke-Powell >Cc: bioconductor@stat.math.ethz.ch >Subject: Re: [BioC] LimmaGUI spot type files > >At 09:42 PM 26/07/2004, Elizabeth Brooke-Powell wrote: > >Hi there, > > > >I was wondering if someone might be able to answer what I hope is a very > >simple question about LimmaGUI's spot type files. > >Do you have to type the full name in the file or can you use partial names > >with an asterisk? For example all of my gene IDs always start with TgEST > >followed by various numbers, can I type TgEST* to identify all genes and > >then * for all controls? All of my controls have different sorts of names. > >Yes, this will work. However you must put the * for controls before the >TgEST* line in your spot types file. > >Gordon >

ADD REPLY • link 19.8 years ago Gordon Smyth 50k