User: Fangxin Hong
Fangxin Hong • 810
- Reputation:
- 810
- Status:
- Trusted
- Location:
- Last seen:
- 12 years, 7 months ago
- Joined:
- 14 years, 7 months ago
- Email:
- f****@salk.edu
Posts by Fangxin Hong
<prev
• 81 results •
page 1 of 9 •
next >
0
votes
3
answers
640
views
3
answers
... 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 12.6 years ago by
Fangxin Hong • 810
0
votes
2
answers
329
views
2
answers
... 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 13.1 years ago by
Fangxin Hong • 810
0
votes
1
answer
355
views
1
answers
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 13.1 years ago by
Fangxin Hong • 810
0
votes
1
answer
355
views
1
answer
...
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 13.1 years ago by
Fangxin Hong • 810
• updated
13.1 years ago by
Ting-Yuan Liu FHCRC • 780
0
votes
4
answers
850
views
4
answers
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 13.1 years ago by
Fangxin Hong • 810
0
votes
4
answers
850
views
4
answers
... 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 13.1 years ago by
Fangxin Hong • 810
0
votes
1
answer
439
views
1
answers
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 13.1 years ago by
Fangxin Hong • 810
0
votes
1
answer
306
views
1
answer
... 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 13.3 years ago by
Fangxin Hong • 810
• updated
13.2 years ago by
Ting-Yuan Liu FHCRC • 780
0
votes
6
answers
716
views
6
answers
... 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 13.3 years ago by
Fangxin Hong • 810
0
votes
1
answer
502
views
1
answers
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 13.3 years ago by
Fangxin Hong • 810
Latest awards to Fangxin Hong
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 161 users visited in the last hour