analysis with no replication
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lidaof ▴ 450
@lidaof-1917
Last seen 6.9 years ago
United States
Hi all, i am doing a Medicago GeneChip with six treated time points without any replication i used limma to analysis that,but the statistic part of Bayesian is not avialable in my condition. and i wanna got the expression curve of each probeset by the time point and select my interested gene with always up regulated for example.Could anyone give some advice on how to do analysis on my condition? for i am really confused. Thank you -- Daofeng Li
Bayesian limma Bayesian limma • 603 views
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@richard-pearson-1304
Last seen 7.1 years ago
Li I'm not sure if I've understand you fully but if you are wanting to identify differentially expressed genes from unreplicated GeneChip data you have a couple of options that I am aware of: 1. The puma package can be used to determine uncertainties in expression levels which can then be used to determine probabilities of differential expression in a principled way. I've not included an unreplicated example in the puma vignette, but this is quite straightforward to do so give me a shout if you'd like to do this with puma but can't figure out how. I believe the bgx package can also do something similar. 2. You could simply apply your favourite summary method, and then use fold change between conditions to determine differentially expressed genes. Having said the above, with unreplicated data you have no information on biological variability, so the ideal approach would be to repeat the experiment if at all possible. Hope that helps Richard. Daofeng Li wrote: > Hi all, > > i am doing a Medicago GeneChip with six treated time points without > any replication > i used limma to analysis that,but the statistic part of Bayesian is > not avialable in my condition. > and i wanna got the expression curve of each probeset by the time > point and select my interested gene with always up regulated for > example.Could anyone give some advice on how to do analysis on my > condition? for i am really confused. > > Thank you > >
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Hi Richard, Thank you for your response. i am reading the manual of puma and will try do some analysis with puma Best! Li On 6/12/07, Richard Pearson <richard.pearson at="" postgrad.manchester.ac.uk=""> wrote: > Li > > I'm not sure if I've understand you fully but if you are wanting to > identify differentially expressed genes from unreplicated GeneChip data > you have a couple of options that I am aware of: > > 1. The puma package can be used to determine uncertainties in expression > levels which can then be used to determine probabilities of differential > expression in a principled way. I've not included an unreplicated > example in the puma vignette, but this is quite straightforward to do so > give me a shout if you'd like to do this with puma but can't figure out > how. I believe the bgx package can also do something similar. > 2. You could simply apply your favourite summary method, and then use > fold change between conditions to determine differentially expressed genes. > > Having said the above, with unreplicated data you have no information on > biological variability, so the ideal approach would be to repeat the > experiment if at all possible. > > Hope that helps > > Richard. > > > Daofeng Li wrote: > > Hi all, > > > > i am doing a Medicago GeneChip with six treated time points without > > any replication > > i used limma to analysis that,but the statistic part of Bayesian is > > not avialable in my condition. > > and i wanna got the expression curve of each probeset by the time > > point and select my interested gene with always up regulated for > > example.Could anyone give some advice on how to do analysis on my > > condition? for i am really confused. > > > > Thank you > > > > > -- Daofeng Li
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