Help: LIMMA-decideTests and lfc option
2
0
Entering edit mode
Sherosha Raj ▴ 90
@sherosha-raj-3225
Last seen 9.6 years ago
Hello everyone I am unsure how to interpret the lfc option in the multiple testing algorithm decideTests: decideTests(object,method="separate",adjust.method="BH",p.value=0.05,l fc=0) The explanation given is: "If lfc>0 then contrasts are judged significant only when the log2-fold change is at least this large in absolute value. For example, one might choose lfc=log2(1.5) to restrict to 50% changes or lfc=1 for 2-fold changes. In this case, contrasts must satisfy both the p-value and the fold-change cutoff to be judged significant." What is meant exactly? Is it within a particular contrast that the log2FC>0 for a particular probeset? Or is it comparing across all the contrasts specified? If some one could offer a clarification I would be most grateful. Thank you. -- Regards, Sherosha -- Regards, Sherosha
• 1.7k views
ADD COMMENT
0
Entering edit mode
Sherosha Raj ▴ 90
@sherosha-raj-3225
Last seen 9.6 years ago
Hi Jim Thank you for the clarification. Is it possible to have a conditional selection based on the lfc in decideTests? Eg. if I had three contrasts and there is a probeset with lfc that satisfies my cutoffs in just ONE contrast but not in the others, and I would still like it to be considered? Thank you again. Regards, Sherosha 2009/1/23 James MacDonald <jmacdon@med.umich.edu> > Hi Sherosha, > > The lfc argument applies to all the contrasts you have made individually. > So for instance if you have three contrasts and for one probeset they were > (-1.5, 0.3, and 1.1) and you set lfc = 1, then the first and third would > pass that filter and the second would not. > > Best, > > Jim > > James W. MacDonald, M.S. > Biostatistician > Hildebrandt Lab > 8220D MSRB III > 1150 W. Medical Center Drive > Ann Arbor MI 48109-0646 > 734-936-8662 > >>> Sherosha Raj <sherosha@gmail.com> 01/22/09 2:28 PM >>> > Hello everyone > > I am unsure how to interpret the lfc option in the multiple testing > algorithm decideTests: > decideTests(object,method="separate",adjust.method="BH",p.value=0.05 ,lfc=0) > > The explanation given is: > "If lfc>0 then contrasts are judged significant only when the > log2-fold change is at least this large in absolute value. For > example, one might choose lfc=log2(1.5) to restrict to 50% changes or > lfc=1 for 2-fold changes. In this case, contrasts must satisfy both > the p-value and the fold-change cutoff to be judged significant." > > What is meant exactly? Is it within a particular contrast that the > log2FC>0 for a particular probeset? Or is it comparing across all the > contrasts specified? > > If some one could offer a clarification I would be most grateful. > Thank you. > > -- > Regards, > Sherosha > > -- > Regards, > Sherosha > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 16 hours ago
United States
I think there is a quote in the fortunes package that covers this: library(fortunes) fortune("yoda") should answer the question of 'Is it possible'. However, if what you really are asking is 'Does decideTests() do a conditional test?', then no. The tests are all on individual contrasts. If you want something different you will have to code it up yourself. Best, Jim James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662 >>> Sherosha Raj <sherosha at="" gmail.com=""> 01/23/09 5:40 PM >>> Hi Jim Thank you for the clarification. Is it possible to have a conditional selection based on the lfc in decideTests? Eg. if I had three contrasts and there is a probeset with lfc that satisfies my cutoffs in just ONE contrast but not in the others, and I would still like it to be considered? Thank you again. Regards, Sherosha 2009/1/23 James MacDonald <jmacdon at="" med.umich.edu=""> > Hi Sherosha, > > The lfc argument applies to all the contrasts you have made individually. > So for instance if you have three contrasts and for one probeset they were > (-1.5, 0.3, and 1.1) and you set lfc = 1, then the first and third would > pass that filter and the second would not. > > Best, > > Jim > > James W. MacDonald, M.S. > Biostatistician > Hildebrandt Lab > 8220D MSRB III > 1150 W. Medical Center Drive > Ann Arbor MI 48109-0646 > 734-936-8662 > >>> Sherosha Raj <sherosha at="" gmail.com=""> 01/22/09 2:28 PM >>> > Hello everyone > > I am unsure how to interpret the lfc option in the multiple testing > algorithm decideTests: > decideTests(object,method="separate",adjust.method="BH",p.value=0.05 ,lfc=0) > > The explanation given is: > "If lfc>0 then contrasts are judged significant only when the > log2-fold change is at least this large in absolute value. For > example, one might choose lfc=log2(1.5) to restrict to 50% changes or > lfc=1 for 2-fold changes. In this case, contrasts must satisfy both > the p-value and the fold-change cutoff to be judged significant." > > What is meant exactly? Is it within a particular contrast that the > log2FC>0 for a particular probeset? Or is it comparing across all the > contrasts specified? > > If some one could offer a clarification I would be most grateful. > Thank you. > > -- > Regards, > Sherosha > > -- > Regards, > Sherosha > > _______________________________________________ > 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 > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]] _______________________________________________ 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENT
0
Entering edit mode
Thanks James. :-) I'll stick to what decideTests offers me : Quote -"Try not. Do, or do not, there is no try." Regards, Sherosha 2009/1/23 James MacDonald <jmacdon@med.umich.edu> > I think there is a quote in the fortunes package that covers this: > > library(fortunes) > fortune("yoda") > > should answer the question of 'Is it possible'. > > However, if what you really are asking is 'Does decideTests() do a > conditional test?', then no. The tests are all on individual contrasts. If > you want something different you will have to code it up yourself. > > Best, > > Jim > > > > James W. MacDonald, M.S. > Biostatistician > Hildebrandt Lab > 8220D MSRB III > 1150 W. Medical Center Drive > Ann Arbor MI 48109-0646 > 734-936-8662 > >>> Sherosha Raj <sherosha@gmail.com> 01/23/09 5:40 PM >>> > Hi Jim > Thank you for the clarification. Is it possible to have a conditional > selection based on the lfc in decideTests? > Eg. if I had three contrasts and there is a probeset with lfc that > satisfies > my cutoffs in just ONE contrast but not in the others, and I would still > like it to be considered? > > > Thank you again. > Regards, > Sherosha > > > 2009/1/23 James MacDonald <jmacdon@med.umich.edu> > > > Hi Sherosha, > > > > The lfc argument applies to all the contrasts you have made individually. > > So for instance if you have three contrasts and for one probeset they > were > > (-1.5, 0.3, and 1.1) and you set lfc = 1, then the first and third would > > pass that filter and the second would not. > > > > Best, > > > > Jim > > > > James W. MacDonald, M.S. > > Biostatistician > > Hildebrandt Lab > > 8220D MSRB III > > 1150 W. Medical Center Drive > > Ann Arbor MI 48109-0646 > > 734-936-8662 > > >>> Sherosha Raj <sherosha@gmail.com> 01/22/09 2:28 PM >>> > > Hello everyone > > > > I am unsure how to interpret the lfc option in the multiple testing > > algorithm decideTests: > > > decideTests(object,method="separate",adjust.method="BH",p.value=0.05 ,lfc=0) > > > > The explanation given is: > > "If lfc>0 then contrasts are judged significant only when the > > log2-fold change is at least this large in absolute value. For > > example, one might choose lfc=log2(1.5) to restrict to 50% changes or > > lfc=1 for 2-fold changes. In this case, contrasts must satisfy both > > the p-value and the fold-change cutoff to be judged significant." > > > > What is meant exactly? Is it within a particular contrast that the > > log2FC>0 for a particular probeset? Or is it comparing across all the > > contrasts specified? > > > > If some one could offer a clarification I would be most grateful. > > Thank you. > > > > -- > > Regards, > > Sherosha > > > > -- > > Regards, > > Sherosha > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > ********************************************************** > > Electronic Mail is not secure, may not be read every day, and should not > be > > used for urgent or sensitive issues > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]
ADD REPLY

Login before adding your answer.

Traffic: 758 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6