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Old 10-10-2008, 07:45 AM   #6
Chema
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Location: Poznan, Poland

Join Date: Jul 2008
Posts: 6
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Hi Victor,

What I wanted to say is that if you have a group of genes that are less expressed in condition 2 than 1, then, you will have less reads that represent these genes in condition 2 than 1, and therefore the genes that are not in this group will be represented for more reads in condition 2 than in condition 1 (not necessarily, because they are differentially expressed). But I guess this problem will be only important when you have a high number of genes differentially expressed.

Yes, you are right the numbers are as you said. Only:

Translate to RPKM , since they have the same length, it should be something like:
Condition 1 Condition 2
Gene A 333,000,000 500,000,000
Gene B 333,000,000 500,000,000
Gene C 333,000,000 0

About if the difference in gene A and B are significant. Well, I didn’t generate any noise for these data, this is a theorical example, they are not estimations if not the real values of the variable. So, if they are different is because the method will declare it as differentially expressed.

Any way, if you want to see a bigger difference, just run an example with more genes that are downregulated in condition 2. You will see that the diference for gene A and B increase.
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