Re: [galaxy-user] cuffdiff fpkm=0 not significant

[Haiping Hao]

ib,

Look at the status column.  I suspect that for this example you given 
the status is HiData.  Cuffdiff considers the expression are very high 
and no statistic testing would have been done for the gene.  fpkm 2=0 
could be misleading, as it may not be actually 0. I have encountered in 
a data set where several genes are expected to be highly expressed in 
all samples, but one of the fpkm values were all given as 0.  Hope this 
helps.


Haiping

--

JHMI Deep Sequencing and Microarray Core Facility at BRB
- Your source for quality service on Microarray studies, NextGen Sequencing, 
and Data Analysis.
http://www.microarray.jhmi.edu/

--


Haiping Hao Ph.D.
Associate Director
Johns Hopkins University Deep Sequencing and Microarray Core
Edward D. Miller Research Building
733 N. Broadway, Rm 359
Baltimore, MD 21205
h...@jhmi.edu
Phone: 443-287-9056
Fax: 410-502-

On 10/15/2012 5:36 PM, i b wrote:

Dear forum,
whoever knows this please tell me!

Given two fpkm  . e.g. fpkm 1=2922828 and fpkm 2=0, why cuffdiff does
not calculate differential expression. those genes are listed in
cuffdiff as not significant and the log2 fold change is infinite ,
either negative or positve...how do i consider them when i want to
pull out the genes that are differentially expressed between treated
and untreated samples?

how do i interpret these data?

thanks,
ib
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/



___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

[galaxy-user] Lost history!

[Haiping Hao]

I had two data file on galaxy and was grooming the data since Monday.  I 
logged in to galaxy today and find my files are all gone.  Any idea what 
happened?


Thank you.

Haiping

--

--

JHMI Deep Sequencing and Microarray Core Facility at BRB
- Your source for quality service on Microarray studies, NextGen Sequencing, 
and Data Analysis.
http://www.microarray.jhmi.edu/

--


Haiping Hao Ph.D.
Manager
Johns Hopkins University Deep Sequencing and Microarray Core
733 N. Broadway, Rm 359
Baltimore, MD 21205
h...@jhmi.edu
Phone: 443-287-9056
Fax: 410-502-

___
The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. For discussion of local Galaxy
instances and the Galaxy source code, please use the
Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other
Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

[galaxy-user] Data upload question

[Haiping Hao]

Hi, I am new to Galaxy and trying to upload some data files.  The size 
of my compressed file is about 7 GB, how long it will take to upload one 
file?


Thank you.

Haiping

--

--

JHMI Deep Sequencing and Microarray Core Facility at BRB
- Your source for quality service on Microarray studies, NextGen Sequencing, 
and Data Analysis.
http://www.microarray.jhmi.edu/

--


Haiping Hao Ph.D.
Manager
Johns Hopkins University Deep Sequencing and Microarray Core
733 N. Broadway, Rm 359
Baltimore, MD 21205
h...@jhmi.edu
Phone: 443-287-9056
Fax: 410-502-

___
The Galaxy User list should be used for the discussion of Galaxy analysis and
other features on the public server at usegalaxy.org.  For discussion of local
Galaxy instances and the Galaxy source code, please use the Galaxy Development
list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the
interface at:

 http://lists.bx.psu.edu/