Re: [galaxy-user] Cuffdiff output

[Ian Donaldson]

I am quite new to RNA-seq analysis, but what I have learned so far is that 
replicates are important.  If you have this result with no replicates then 
P-values are more or less meaningless.  You can also gauge what is happening by 
looking at the modelled read count output.  If the counts are both less than 
50ish you are unlikely to have a robust result for that gene/transcript.

Ian 



From: galaxy-user-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] on behalf of Malik, Shivani 
[shivani.ma...@ucsf.edu]
Sent: 11 March 2014 21:43
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Cuffdiff output

Hi,
I have a question about interpreting the cuffdiff data and how to pick up 
significant genes. I have genes which show ~8 fold change between 2 conditions: 
eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is 
threshold of FPKM below which Cuffdiff does not consider it  an FPKM to be 
valid and hence significance in no? What downstream analysis should I use to 
extract a meaningful list of genes from the Cuffdiff data?

Also, I filtered out FPKMs which were below 5 in both conditions? Is that 
reasonable?

Thanks
Shivani



___
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

___
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

[galaxy-user] Cuffdiff output

[Malik, Shivani]

Hi,
I have a question about interpreting the cuffdiff data and how to pick up 
significant genes. I have genes which show ~8 fold change between 2 conditions: 
eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is 
threshold of FPKM below which Cuffdiff does not consider it  an FPKM to be 
valid and hence significance in no? What downstream analysis should I use to 
extract a meaningful list of genes from the Cuffdiff data? 

Also, I filtered out FPKMs which were below 5 in both conditions? Is that 
reasonable?

Thanks
Shivani



___
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/