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Phil A
Phil A
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As you say, you're asking two distinct questions.

Question 1 "is the ratio L*/L1+ different from B*/B1+ for a given gene function"

this might be best answered with Fisher's exact test using data across the row as you found previously.

Question 2 "is the ratio: genes where there is a single copy / genes where there is more than one copy, different between gene functions?"

I think this also might be best answered with Fisher's exact test. You'd test the ratio of L*/L1+ for gene function 1 against L*/L1+ for gene function 2. Then gene function 1 Vs gene function 3, etc.

Neither of these sets of questions gets at whether or not they are being maintained/deleted faster than expected purely by chance, only whether they are being deleted/maintained at rates different from each other. To answer thatknow if they were being deleted/maintained at a rate different than by chance, you'd need to know the ratio of singlecopy/multiplecopies for lots of DNA regions that are only being affectedaffected by chance. SoIf you could find such regions, you'd end up with a Function group of"Function group" where function is "None" which you'd. You'd then compare this to your other gene function groups in the same way as I described in question 2.

As you say, you're asking two distinct questions.

Question 1 "is the ratio L*/L1+ different from B*/B1+ for a given gene function"

this might be best answered with Fisher's exact test using data across the row as you found previously.

Question 2 "is the ratio: genes where there is a single copy / genes where there is more than one copy, different between gene functions?"

I think this also might be best answered with Fisher's exact test. You'd test the ratio of L*/L1+ for gene function 1 against L*/L1+ for gene function 2. Then gene function 1 Vs gene function 3, etc.

Neither of these sets of questions gets at whether or not they are being maintained/deleted faster than expected purely by chance. To answer that you'd need to know the ratio of singlecopy/multiplecopies for lots of DNA regions that are only being affected by chance. So you'd end up with a Function group of "None" which you'd compare to your other gene function groups.

As you say, you're asking two distinct questions.

Question 1 "is the ratio L*/L1+ different from B*/B1+ for a given gene function"

this might be best answered with Fisher's exact test using data across the row as you found previously.

Question 2 "is the ratio: genes where there is a single copy / genes where there is more than one copy, different between gene functions?"

I think this also might be best answered with Fisher's exact test. You'd test the ratio of L*/L1+ for gene function 1 against L*/L1+ for gene function 2. Then gene function 1 Vs gene function 3, etc.

Neither of these sets of questions gets at whether or not they are being maintained/deleted faster than expected purely by chance, only whether they are being deleted/maintained at rates different from each other. To know if they were being deleted/maintained at a rate different than by chance, you'd need to know the ratio of singlecopy/multiplecopies for lots of DNA regions that are only being affected by chance. If you could find such regions, you'd end up with a "Function group" where function is "None". You'd then compare this to your other gene function groups in the same way as I described in question 2.

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Phil A
Phil A
  • 21
  • 4

As you say, you're asking two distinct questions.

Question 1 "is the ratio L*/L1+ different from B*/B1+ for a given gene function"

this might be best answered with Fisher's exact test using data across the row as you found previously.

Question 2 "is the ratio: genes where there is a single copy / genes where there is more than one copy, different between gene functions?"

I think this also might be best answered with Fisher's exact test. You'd test the ratio of L*/L1+ for gene function 1 against L*/L1+ for gene function 2. Then gene function 1 Vs gene function 3, etc.

Neither of these sets of questions gets at whether or not they are being maintained/deleted faster than expected purely by chance. To answer that you'd need to know the ratio of singlecopy/multiplecopies for lots of DNA regions that are only being affected by chance. So you'd end up with a Function group of "None" which you'd compare to your other gene function groups.