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
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
>
>
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
