User: Fangxin Hong
Fangxin Hong • 810
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Posts by Fangxin Hong
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... Dear Weiwei,
The definition of outlier is not clear, and no data point should be
treated as outlier unless there is reason to believe so. The simple
way to
detect it is that 1.5IQR criteria, which you can write your own code
(one
or two lines). Update me if there are any other method to detect
outli ...
written 12.0 years ago by
Fangxin Hong • 810
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... If you are interested in finding DE (differetially expressed ) genes,
you
can try RankProd, which combines data from different platforms without
assuming equal variance. For linear model without assuming equal
variance,
it sounds to me that you shouldn't use one linear model since you
won't
gain an ...
written 12.5 years ago by
Fangxin Hong • 810
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Comment:
C: Arabidopsis annotation package
... Hi Ting-Yuan,
Thank you for your reply.
>
> The package ath1121501 (version 1.10.0) is built by the public data
we
> collected on September 29, 2005. Any updated information on the
data
> website after September 29, 2005 would not be included in the
package
> ath1121501 (version 1. ...
written 12.5 years ago by
Fangxin Hong • 810
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...
Hi there,
I met some questions about arabidopsis annotation package(ath1121501,
version 1.10), I will
be truly grateful if any of you can help me with some questions.
(1) I tried to get PUBMED ID for probesets (Affy) that have known
function
and known pubmed ID from website. However, the "ath112 ...
written 12.5 years ago by
Fangxin Hong • 810
• updated 12.5 years ago by
Ting-Yuan Liu FHCRC • 780
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Comment:
C: Analysis for only 2 replicates
... Based on my experience,SAM usually fails with only 2 replicates under
each
condition.
Limma and RankProd both can handle 2 replicates.
Fangxin
>
>
>
> On 3/8/06 4:07 PM, "Khan, Sohail" wrote:
>
>> Dear list,
>>
>> I have 2 -wt and 2-mutant samples done on Affymetr ...
written 12.6 years ago by
Fangxin Hong • 810
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... try Rankprod which is based on fold change but with much more power.
Fangxin
> Dear list,
>
> I have 2 -wt and 2-mutant samples done on Affymetrix chips.
> Could you suggest the best way to analyze this experiment? Is
averaging
> both replicates and picking genes based on fold chang ...
written 12.6 years ago by
Fangxin Hong • 810
0
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Answer:
A: Rank Product
... Hi Nadine,
> 1. I tried to calculate the Rank product in Excell (as explain in
the
> paper
> of Rainer Breitling) using a small data set, i didn't get the same
> results
> as calculating it with R-Programm.
> Can somebody help me?
The RankProd package under bioconductor is progra ...
written 12.6 years ago by
Fangxin Hong • 810
0
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... Hi list,
Does anyone know whether ath1121501 package has been updated to
include
additional information, such as "ath1121501CHRLENGTHS" ? Without it,
geneplotter package is not applicable. I think such informaion is
available from TAIR.
Thanks!
Fangxin
--------------------
Fangxin Hong Ph.D.
P ...
written 12.7 years ago by
Fangxin Hong • 810
• updated 12.7 years ago by
Ting-Yuan Liu FHCRC • 780
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... Thank you all for the useful input and interesting discussion.
I agree with Henk, "biologicla replicates" means to include biological
variation among individual plants, not the enviromental factors, such
as
growth chamber and climate. It is known that batch effect and lab
effect
are profound factor ...
written 12.7 years ago by
Fangxin Hong • 810
0
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437
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Answer:
A: RNA degradation problem
... Hi Matthew,
Thank you very much for your help.
> It's amazing how many
> lab plant biologists see pooled samples from a bulk of plants grown
at
> the same time as biological replicates when they are clearly not.
I would think that all plants under experiment shoudl be grown at the
same
ti ...
written 12.7 years ago by
Fangxin Hong • 810
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