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Input data structure for SAMseq slowsmile Bioinformatics 8 12-11-2015 03:16 PM

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Old 11-02-2012, 03:08 AM   #1
narges
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Location: Finland

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Default SAMseq

Hi all,
The SAMseq output produces down and up regulated genes separately listed.
If I want to retrieve the first 1000 DE genes regardless the idea of up or down regulated, which property do you offer to sort the genes according to. The q-value, score or fold change?
Or for example do you think between these two genes which one has higher priority when choosing DE genes:
Genes down
Gene ID Gene Name Score(d) Fold Change q-value(%)
[1,] g22 22 -8 0.483 32.045

Genes up
Gene ID Gene Name Score(d) Fold Change q-value(%)
[307,] g21217 21217 7.75 2.578 18.555

Should I choose the up regulated one which is 307th DE up regulated gene but with lower q=value or choose the first down regulated one with score equal to 8 but q=value equal to 32.045?
Many thanks in advance.
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