Question: Queries regarding cuffdiff output especially gene_exp_diff (Tumor and Normal) no replicates
0
gravatar for bioinforesearchquestions
2.7 years ago by
United States
bioinforesearchquestions230 wrote:

Dear All,

I am working on RNAseq data. I am comparing tumor and normal samples. I got this output file from cuffdiff step.

I would like to understand about this output file.

gene_exp.diff - Gene level differential expression. Tests differences in the summed FPKM of transcripts sharing each gene_id.

If you have any document discussing the below things, kindly refer it. Thanks in advance.

I have following queries,

  • value1 is FPKMx and value2 is FPKMy

  • Log2(fold-change) => log((6.04054/158.412),2) is -4.71286 for gene MUC1. Refer row 6 in the below image.

- How to calculate test-stat by comparing one value from each sample?

- What is the threshold value used to categorize genes as "significant" and "non-significant"?

  • For example, I noticed the following fold change for the below genes are referred as SIGNIFICANT

**DMBX1 : 0/3.51818 is -infinite fold change

SPRR2F : 45.7115/0 is infinite fold change MUC1 : 6.040/158.412 ( sample1 is 25 times higher than sample 2)

ADAM12 : 0.592487/100.418 ( sample1 is ~100 times more than sample2)

VEGFA : 2.49672/57.0407 ( sample1 is ~27 times more than sample2)

ADGRG2 : 0.119485/8.46 (sample1 is ~7 times more than sample2)**

  • For example, I noticed the following fold change for the below genes are referred as NON-SIGNIFICANT

**AGRN1 : 6.30387/57.554 (sample1 is ~9times higher than sample2)

MMP23B : 22.1959/9.17679 (sample1 is ~2.5times lower than sample2)

LINCO1128: 3.11434/1.87709 (sample1 is ~1.5 times lower than sample2)**

https://i.imgsafe.org/190431586c.png

enter image description here

rna-seq • 1.2k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by bioinforesearchquestions230
1
gravatar for igor
2.7 years ago by
igor7.7k
United States
igor7.7k wrote:

The cuffdiff manual explains the output in detail. Link: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#differential-expression-tests ("Differential expression tests" section)

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by igor7.7k

Thanks, igor +1 for the link. Can you help with the below queries

  • How to calculate test-stat? (b'cos in my case, I dont' have replicates)
  • What is the threshold value used to categorize genes as "significant" and "non-significant"?
ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by bioinforesearchquestions230
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