Hi,
   I think it will depend on what genes you are looking at and what is the
expected expression levels of these genes. If is a low copy number gene,
for example a olfaction gene or a GPCR, it expression levels might not
change a lot. I saw some publications where they consider FPKM higher than
1. I consider log2fold change >2, FPKM >1, FDR >0.05, and its biological
significance as well as the tissue you are analyzing. Sometimes heat-maps
can give you a better idea of expression patterns of functional groups of
genes over time series data.
Luciano


On Wed, Sep 19, 2012 at 5:28 PM, Du, Jianguang <jia...@iupui.edu> wrote:

>  Dear All,
>
> I am comparing the gene expression between two cell types by examining the
> Cufflink output file -- gene differential expression testing. The file
> lists the FPKM of genes in two cell types and log2 of fold. I want to look
> for genes that have more than 2-flod of expression in cell type A than in
> cell type B. What is the minimum FPKM in cell type A so that only the genes
> that have FPKM highier than this number can be taken into consideration for
> further analysis?
>
> For example,
>
> The FPKM of gene X in cell type A is 80, and in cell type B is 20,
> the fold of difference is 4.
>
> The FPKM of gene Y in cell type A is 4, and in cell type B is 1, the fold
> of difference is also 4.
>
> Is there a minimum FPKM in cell type A for genes to be selected for
> further analysis?
>
> Thanks.
>
> Jianguang
>
> ___________________________________________________________
> 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/
>



-- 
*Luciano Cosme*

---------------------------------------------
PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
www.lcosme.com
979 845 1885
co...@tamu.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/

Reply via email to