Question: skewed cuffdiff result
2
gravatar for kint1007
4.1 years ago by
kint100720
Korea, Republic Of
kint100720 wrote:

Hi,

I hava a question about using Cuffdiff with mouse single-end reads.

I get result (gene_exp.diff) skewed differential expressed genes (up: 113, down: 579).

That is wierd.

So, I count the gene to check the whole expression is skewed.

  log2FC   FPKM == 0   NOTEST LOWDATA   |FC| < 1.2 (mid)       yes  
DOWN < 0 9411 419 (Stress FPKM == 0 )  = 8992 2139 14 = 6839 1495 = 5344   ...  579  
  == 0 4502 both 0                    
UP > 0 10084 710 Inf(control FPKM=0)  = 9374 1523 26 = 7825 892 = 6933   ...  113  

 

remove FPKM = 0, NOTEST, LOWDATA ,

The number is similar. (6839, 7825)

Even after remove |FC| < 1.2, DOWN expression is 5344 and UP expression is 6933.

I wonder what reasons?

When cuffdiff calculate pvalue and qvalue, is there some filter option or something?

Thank you,

sequencing rna-seq gene • 965 views
ADD COMMENTlink modified 4.1 years ago by Ido Tamir5.0k • written 4.1 years ago by kint100720
1
gravatar for Ido Tamir
4.1 years ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:

You could try some diagnostic plots like MA or FPKM/FPKM or FPKM density across replicates etc, if you see a bias (with or without normalisation). Were the samples prepared in the same batch? If you don't see a bias and the samples were prepared in the same batch, and you see deregulation in mostly one direction - why do you think its biologically wrong?

 

 

 

 

 

ADD COMMENTlink written 4.1 years ago by Ido Tamir5.0k
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