minimum expression level (Simpleaffy)
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@patricia-luiza-nunes-da-costa-2595
Last seen 7.7 years ago
Hi group! After normalization of expression data, using SimpleAffy, we observed low fluorescence intensities to every probesets, between 2,15 and 14,6 (mean= 5,78). What value should I set to minimum expression level? For Affymetrix experiments, the default here has been set at log2(10), but I think it seems very stringent to my data, what do you think? Thanks and regards, Patr?cia Patr?cia Luiza Nunes da Costa Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular Faculdade de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112 Cerqueira Cesar Cep 01246-903 Tel: (11) 3061-7486 e (11) 8202-7073 Patr?cia Luiza Nunes da Costa Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular Faculdade de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112 Cerqueira Cesar Cep 01246-903 Tel: (11) 3061-7486 e (11) 8202-7073 -------------------------- Esta mensagem foi verificada pelo sistema de antiv?rus DIM e acredita-se estar livre de Virus.
Normalization simpleaffy Normalization simpleaffy • 635 views
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alex lam RI ▴ 310
@alex-lam-ri-1491
Last seen 7.7 years ago
Hi Patricia, Between 2.15 - 14.6 sounds about right. Remember the intensities are in log scale after GCRMA or RMA. In my last affymetrix analysis I think I used ~ 3.5. It was decided in an ad-hoc way by looking at the distributions: those under this threshold in my dataset also had very low variability across samples. 10 seems very stringent cut-off to me. Making plots of your data can help you decide what threshold to use. Best wishes, Alex -------------------------------------------- Alex C. Lam Roslin Institute (Edinburgh) Midlothian EH25 9PS United Kingdom Tel: +44 131 5274471 Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Patr?cia Luiza Nunes da Costa Sent: 28 January 2008 13:12 To: bioconductor at stat.math.ethz.ch Subject: [BioC] minimum expression level (Simpleaffy) Hi group! After normalization of expression data, using SimpleAffy, we observed low fluorescence intensities to every probesets, between 2,15 and 14,6 (mean= 5,78). What value should I set to minimum expression level? For Affymetrix experiments, the default here has been set at log2(10), but I think it seems very stringent to my data, what do you think? Thanks and regards, Patr?cia Patr?cia Luiza Nunes da Costa Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular Faculdade de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112 Cerqueira Cesar Cep 01246-903 Tel: (11) 3061-7486 e (11) 8202-7073 Patr?cia Luiza Nunes da Costa Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular Faculdade de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112 Cerqueira Cesar Cep 01246-903 Tel: (11) 3061-7486 e (11) 8202-7073 -------------------------- Esta mensagem foi verificada pelo sistema de antiv?rus DIM e acredita-se estar livre de Virus. _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Alex! Thanks for your suggestions! I think I understood. But, I don?t know how to make these plots (I?m a new user of ?R?). Do you have any manual or exercise that could help me? I?ve tried to make its using simpleaffy commands, but it doesn?t work. I had the error below: plot(significant, type="scatter") Error in .local(x, y, ...) : unused argument(s) (type = "scatter") Thanks again!!! Patricia > Hi Patricia, > Between 2.15 - 14.6 sounds about right. Remember the intensities are in > log scale after GCRMA or RMA. > > In my last affymetrix analysis I think I used ~ 3.5. It was decided in an > ad-hoc way by looking at the distributions: those under this threshold in > my dataset also had very low variability across samples. 10 seems very > stringent cut-off to me. Making plots of your data can help you decide > what threshold to use. > > Best wishes, > Alex > > -------------------------------------------- > Alex C. Lam > Roslin Institute (Edinburgh) > Midlothian > EH25 9PS > United Kingdom > Tel: +44 131 5274471 > > Roslin Institute is a company limited by guarantee, registered in Scotland > (registered number SC157100) and a Scottish Charity (registered number > SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT > registration number 847380013. > > The information contained in this e-mail (including any attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are the > opinions of the sender and do not necessarily constitute those of Roslin > Institute (Edinburgh) ("the Institute") unless specifically stated by a > sender who is duly authorised to do so on behalf of the Institute > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Patr?cia > Luiza Nunes da Costa > Sent: 28 January 2008 13:12 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] minimum expression level (Simpleaffy) > > Hi group! > > After normalization of expression data, using SimpleAffy, we observed low > fluorescence intensities to every probesets, between 2,15 and 14,6 (mean= > 5,78). > What value should I set to minimum expression level? > For Affymetrix experiments, the default here has been set at log2(10), but > I think it seems very stringent to my data, what do you think? > > Thanks and regards, > Patr?cia > > > > Patr?cia Luiza Nunes da Costa > Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular Faculdade > de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112 > Cerqueira Cesar Cep 01246-903 > Tel: (11) 3061-7486 e (11) 8202-7073 > > > > > Patr?cia Luiza Nunes da Costa > Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular Faculdade > de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112 > Cerqueira Cesar Cep 01246-903 > Tel: (11) 3061-7486 e (11) 8202-7073 > > > > -------------------------- > Esta mensagem foi verificada > pelo sistema de antiv?rus DIM e > acredita-se estar livre de Virus. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -------------------------- > Esta mensagem foi verificada > pelo sistema de antiv?rus DIM e > acredita-se estar livre de Virus. > Patr?cia Luiza Nunes da Costa Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular Faculdade de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112 Cerqueira Cesar Cep 01246-903 Tel: (11) 3061-7486 e (11) 8202-7073 -------------------------- Esta mensagem foi verificada pelo sistema de antiv?rus DIM e acredita-se estar livre de Virus.
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Hi Patricia, The exprs() function will return a matrix of expression values, with rows being probesets, and columns being samples. For example you can get the mean expression value for each probeset like this: apply(exprs(your.eset.object), 1, mean) This will give you one value per probeset. Then, for example, you can plot a histogram using hist() to inspect the expression distribution. Apart from mean, you can also look at statistics like median or max to decide what is the cut off for low signal. Good luck, Alex -----Original Message----- From: Patr?cia Luiza Nunes da Costa [mailto:patriciacosta@lim24.fm.usp.br] Sent: 28 January 2008 16:18 To: alex lam (RI) Cc: bioconductor at stat.math.ethz.ch Subject: RE: [BioC] minimum expression level (Simpleaffy) Hi Alex! Thanks for your suggestions! I think I understood. But, I don't know how to make these plots (I'm a new user of "R"). Do you have any manual or exercise that could help me? I've tried to make its using simpleaffy commands, but it doesn't work. I had the error below: plot(significant, type="scatter") Error in .local(x, y, ...) : unused argument(s) (type = "scatter") Thanks again!!! Patricia > Hi Patricia, > Between 2.15 - 14.6 sounds about right. Remember the intensities are > in log scale after GCRMA or RMA. > > In my last affymetrix analysis I think I used ~ 3.5. It was decided in > an ad-hoc way by looking at the distributions: those under this > threshold in my dataset also had very low variability across samples. > 10 seems very stringent cut-off to me. Making plots of your data can > help you decide what threshold to use. > > Best wishes, > Alex > > -------------------------------------------- > Alex C. Lam > Roslin Institute (Edinburgh) > Midlothian > EH25 9PS > United Kingdom > Tel: +44 131 5274471 > > Roslin Institute is a company limited by guarantee, registered in > Scotland (registered number SC157100) and a Scottish Charity > (registered number SC023592). Our registered office is at Roslin, > Midlothian, EH25 9PS. VAT registration number 847380013. > > The information contained in this e-mail (including any attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Patr?cia > Luiza Nunes da Costa > Sent: 28 January 2008 13:12 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] minimum expression level (Simpleaffy) > > Hi group! > > After normalization of expression data, using SimpleAffy, we observed > low fluorescence intensities to every probesets, between 2,15 and 14,6 > (mean= 5,78). > What value should I set to minimum expression level? > For Affymetrix experiments, the default here has been set at log2(10), > but I think it seems very stringent to my data, what do you think? > > Thanks and regards, > Patr?cia > > > > Patr?cia Luiza Nunes da Costa > Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular > Faculdade de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, > 455 sala 4112 Cerqueira Cesar Cep 01246-903 > Tel: (11) 3061-7486 e (11) 8202-7073 > > > > > Patr?cia Luiza Nunes da Costa > Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular > Faculdade de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, > 455 sala 4112 Cerqueira Cesar Cep 01246-903 > Tel: (11) 3061-7486 e (11) 8202-7073 > > > > -------------------------- > Esta mensagem foi verificada > pelo sistema de antiv?rus DIM e > acredita-se estar livre de Virus. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -------------------------- > Esta mensagem foi verificada > pelo sistema de antiv?rus DIM e > acredita-se estar livre de Virus. > Patr?cia Luiza Nunes da Costa Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular Faculdade de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112 Cerqueira Cesar Cep 01246-903 Tel: (11) 3061-7486 e (11) 8202-7073 -------------------------- Esta mensagem foi verificada pelo sistema de antiv?rus DIM e acredita-se estar livre de Virus.
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