LimmaGUI discards spots with no signal on one channel?

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Gordon Smyth 52k

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> Date: Fri, 08 Apr 2005 15:56:39 +0100 > From: J.delasHeras@ed.ac.uk > Subject: [BioC] LimmaGUI discards spots with no signal on one > channel?? > To: bioconductor@stat.math.ethz.ch > > > I am a recent user of the LimmaGUI package. I searched the archives and couldn't > find this issue raised, so I hope somebody can help. > > I'm finding that LimmaGUI works very well to look at what genes are > differentially expressed, as long as they are expressed to some extent on both > samples (channels). I am currently mainly interested in extremes of expression: > looking at genes that are inactive in one sample, but active in the other, and > I'm finding that LimmaGUI is disregarding all those genes that have no signal > on one channel (no matter how strong the signal on the other)... so all the > genes that I want are out of the list of differentially expressed genes. This is a characteristic of local background correction, it is not specifically a characteristic of limmaGUI. It has everything to do with with the choice of image analysis program and background estimator that you're using. > How could I get around this? 1. Don't background correct, or 2. Use a background correction option which ensures positive corrected intensities, or 3. Switch to an image analysis program with a low stable background estimator available, e.g, SPOT or GenePix 6 with morph background. The authors of limma and limmaGUI always do 2. or 3. in their own work, because of the sort of problem that you mention. Gordon > Jose > > -- > Dr. Jose I. de las Heras Email: J.delasHeras@ed.ac.uk > The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 > Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 > Swann Building, Mayfield Road > University of Edinburgh > Edinburgh EH9 3JR > UK

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ADD COMMENT • link 19.7 years ago • updated 19.6 years ago Gordon Smyth 52k

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J.delasHeras@ed.ac.uk ★ 1.9k

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Quoting Gordon K Smyth <smyth@wehi.edu.au>: > This is a characteristic of local background correction, it is not > specifically a characteristic > of limmaGUI. It has everything to do with with the choice of image analysis > program and > background estimator that you're using. > > > How could I get around this? > > 1. Don't background correct, or > 2. Use a background correction option which ensures positive corrected > intensities, or > 3. Switch to an image analysis program with a low stable background estimator > available, e.g, SPOT > or GenePix 6 with morph background. > > The authors of limma and limmaGUI always do 2. or 3. in their own work, > because of the sort of > problem that you mention. > > Gordon bingo! :-) thank you *soooo much* for a great and FAST reply... Jose -- Dr. Jose I. de las Heras Email: J.delasHeras@ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK

ADD COMMENT • link 19.7 years ago J.delasHeras@ed.ac.uk ★ 1.9k

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Ramon Diaz ★ 1.1k

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Dear Gordon, > > This is a characteristic of local background correction, it is not > specifically a characteristic of limmaGUI. It has everything to do with > with the choice of image analysis program and background estimator that > you're using. > > > How could I get around this? > > 1. Don't background correct, or > 2. Use a background correction option which ensures positive corrected > intensities, or 3. Switch to an image analysis program with a low stable > background estimator available, e.g, SPOT or GenePix 6 with morph > background. > > The authors of limma and limmaGUI always do 2. or 3. in their own work, > because of the sort of problem that you mention. Is there any guidance (paper, tech. report, your experience) on how to choose among the options available in limma for backgroundCorrect that implement 2. (i.e., half, minimum, edwards or normexp)? Thanks, R. > > Gordon > > > Jose > > > > -- > > Dr. Jose I. de las Heras Email: > > J.delasHeras@ed.ac.uk The Wellcome Trust Centre for Cell Biology > > Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology > > Fax: +44 (0)131 6507360 Swann Building, Mayfield Road > > University of Edinburgh > > Edinburgh EH9 3JR > > UK > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

ADD COMMENT • link 19.6 years ago Ramon Diaz ★ 1.1k

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Gordon Smyth 52k

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> Date: Mon, 18 Apr 2005 11:06:03 +0200 > From: "Ramon Diaz-Uriarte" <rdiaz@cnio.es> > Subject: Re: [BioC] LimmaGUI discards spots with no signal on one > channel? > To: <bioconductor@stat.math.ethz.ch>, <smyth@wehi.edu.au> > Cc: J.delasHeras@ed.ac.uk > > Dear Gordon, > >> >> This is a characteristic of local background correction, it is not >> specifically a characteristic of limmaGUI. It has everything to do with >> with the choice of image analysis program and background estimator that >> you're using. >> >> > How could I get around this? >> >> 1. Don't background correct, or >> 2. Use a background correction option which ensures positive corrected >> intensities, or 3. Switch to an image analysis program with a low stable >> background estimator available, e.g, SPOT or GenePix 6 with morph >> background. >> >> The authors of limma and limmaGUI always do 2. or 3. in their own work, >> because of the sort of problem that you mention. > > Is there any guidance (paper, tech. report, Not yet. > your experience) I currently use SPOT or GenePix 6 with morph background. If I have to use local background, then I use normexp with a small offset. There is an illustration of the effectness this in the Limma User's Guide. Gordon > on how to choose > among the options available in limma for backgroundCorrect that implement 2. > (i.e., half, minimum, edwards or normexp)? > > > Thanks, > > R. > > > >> >> Gordon >> >> > Jose >> > >> > -- >> > Dr. Jose I. de las Heras Email: >> > J.delasHeras@ed.ac.uk The Wellcome Trust Centre for Cell Biology >> > Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology >> > Fax: +44 (0)131 6507360 Swann Building, Mayfield Road >> > University of Edinburgh >> > Edinburgh EH9 3JR >> > UK

ADD COMMENT • link 19.6 years ago Gordon Smyth 52k

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Thanks a lot for the answer, Gordon. Best, R. On Monday 18 April 2005 13:33, Gordon K Smyth wrote: > > Date: Mon, 18 Apr 2005 11:06:03 +0200 > > From: "Ramon Diaz-Uriarte" <rdiaz@cnio.es> > > Subject: Re: [BioC] LimmaGUI discards spots with no signal on one > > channel? > > To: <bioconductor@stat.math.ethz.ch>, <smyth@wehi.edu.au> > > Cc: J.delasHeras@ed.ac.uk > > > > > > Dear Gordon, > > > >> This is a characteristic of local background correction, it is not > >> specifically a characteristic of limmaGUI. It has everything to do with > >> with the choice of image analysis program and background estimator that > >> you're using. > >> > >> > How could I get around this? > >> > >> 1. Don't background correct, or > >> 2. Use a background correction option which ensures positive corrected > >> intensities, or 3. Switch to an image analysis program with a low stable > >> background estimator available, e.g, SPOT or GenePix 6 with morph > >> background. > >> > >> The authors of limma and limmaGUI always do 2. or 3. in their own work, > >> because of the sort of problem that you mention. > > > > Is there any guidance (paper, tech. report, > > Not yet. > > > your experience) > > I currently use SPOT or GenePix 6 with morph background. If I have to use > local background, then I use normexp with a small offset. There is an > illustration of the effectness this in the Limma User's Guide. > > Gordon > > > on how to choose > > among the options available in limma for backgroundCorrect that implement > > 2. (i.e., half, minimum, edwards or normexp)? > > > > > > Thanks, > > > > R. > > > >> Gordon > >> > >> > Jose > >> > > >> > -- > >> > Dr. Jose I. de las Heras Email: > >> > J.delasHeras@ed.ac.uk The Wellcome Trust Centre for Cell Biology > >> > Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology > >> > Fax: +44 (0)131 6507360 Swann Building, Mayfield Road > >> > University of Edinburgh > >> > Edinburgh EH9 3JR > >> > UK -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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