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xiaolei-lab / hiblup

:surfer: HIBLUP is an Integration of Statistical Methods Under BLUP Framework for Genomic Selection and Prediction
https://www.hiblup.com
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Errors in pedigree based relationship matrix (A matrix) in HIBLUP #2

Open balathumma10 opened 4 years ago

balathumma10 commented 4 years ago

Hi, I am trying to use HIBLUP package to estimate breeding values. However it looks like the results of pedigree based A matrix are not quite right. I have three generation pedigree data from only maternal parent (grand mother, mother and progeny) side. The output from additive relationship matrix does not reflect the pedigree file. For example when there is a grand mother for a mother, the A matrix shows zero between grand mother and mother instead of 0.5.

Please let me know if you need the pedigree file if you want to replicate the problem.

Thank you.

XiaoleiLiuBio commented 4 years ago

Hi,

Thank you very much for pointing out the issue. Could you please send me the pedigree file?

Regards, Xiaolei

---------- Origin message ----------

From："balathumma10" notifications@github.com To："xiaolei-lab/hiblup" hiblup@noreply.github.com Subject：[xiaolei-lab/hiblup] Errors in pedigree based relationship matrix (A matrix) in HIBLUP (#2) Date：2020-01-28 08:36:41Hi, I am trying to use HIBLUP package to estimate breeding values. However it looks like the results of pedigree based A matrix are not quite right. I have three generation pedigree data from only maternal parent (grand mother, mother and progeny) side. The output from additive relationship matrix does not reflect the pedigree file. For example when there is a grand mother for a mother, the A matrix shows zero between grand mother and mother instead of 0.5.

Please let me know if you need the pedigree file if you want to replicate the problem.

Thank you.

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/xiaolei-lab/hiblup/issues/2

balathumma10 commented 4 years ago

Hi Xiaolei Thanks for the quick response. Here is the pedigree file.

Thank you, Best regards Bala

On Tue, Jan 28, 2020 at 11:57 AM Xiaolei Liu notifications@github.com wrote:

Hi,

Thank you very much for pointing out the issue. Could you please send me the pedigree file?

Regards, Xiaolei

---------- Origin message ----------

From："balathumma10" notifications@github.com To："xiaolei-lab/hiblup" hiblup@noreply.github.com Subject：[xiaolei-lab/hiblup] Errors in pedigree based relationship matrix (A matrix) in HIBLUP (#2) Date：2020-01-28 08:36:41Hi, I am trying to use HIBLUP package to estimate breeding values. However it looks like the results of pedigree based A matrix are not quite right. I have three generation pedigree data from only maternal parent (grand mother, mother and progeny) side. The output from additive relationship matrix does not reflect the pedigree file. For example when there is a grand mother for a mother, the A matrix shows zero between grand mother and mother instead of 0.5.

Please let me know if you need the pedigree file if you want to replicate the problem.

Thank you.

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/xiaolei-lab/hiblup/issues/2

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/hiblup/issues/2?email_source=notifications&email_token=AHQKHT2YQ23GSPURU3Y7YJLQ757HVA5CNFSM4KMKPP52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEKBUSNA#issuecomment-579029300, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHQKHTY2ZNEPYTCAAXOXXKTQ757HVANCNFSM4KMKPP5Q .

XiaoleiLiuBio commented 4 years ago

I didn't see the pedigree file. Could you please send it to xiaoleiliu@mail.hzau.edu.cn?

XiaoleiLiuBio commented 4 years ago

Hi Bala,

Thank you for providing me the data. We have checked but didn't find the error. Could you please send me an example of the wrong position in A matrix?

Please mention that the users don't need to sort the individuals in the pedigree file by birth date before using HIBLUP. This also means that the order of individuals in the output A matrix file maybe not the same as the pedigree file.

Regards, Xiaolei