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Old 01-14-2013, 05:17 PM   #1
Richard.Y
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Default cuffdiff significantly differently expressed genes

I got too few significantly differently expressed genes between two samples, was something wrong. and how did cuffdiff call a gene significantly differently expressed
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Old 01-14-2013, 05:24 PM   #2
chadn737
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1) How do you know its too few?

2) "two samples" do you mean multiple biological replicates of two conditions or only two samples? It makes a big difference.
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Old 01-14-2013, 07:46 PM   #3
Richard.Y
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1)I got just 68 genes significantly differently expressed
2) one is cancer cell line,the other is normal tissue
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Old 01-14-2013, 07:46 PM   #4
Richard.Y
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Quote:
Originally Posted by chadn737 View Post
1) How do you know its too few?

2) "two samples" do you mean multiple biological replicates of two conditions or only two samples? It makes a big difference.
1)I got just 68 genes significantly differently expressed
2) one is cancer cell line,the other is normal tissue
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Old 01-14-2013, 07:49 PM   #5
chadn737
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1) Why is 68 too few?

2) So you have only two samples, no replicates?
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