Missing phenotypes

laavanya rayaprolu

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Sep 5, 2022, 9:15:49 AM9/5/22

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Hi Karl

I am using a backcross population and I do not have the data for all the phenotypes. The results are different if I use "NA" for a missing phenotype and when I completely remove the phenotype from the input file (attached below). Please suggest what could be the reason and what can be done.

Regards

Laavanya Rayaprolu

phiPSII_12.1.png

phiPSII_12.1_missingphenotyperemoved.png

Karl Broman

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Sep 6, 2022, 11:18:43 AM9/6/22

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I'm not sure I understand. The two plots look identical to me, and I would expected them to be identical. In QTL analysis, any individuals with missing phenotype are omitted, as they provide no information.

karl

laavanya rayaprolu

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Sep 6, 2022, 4:20:58 PM9/6/22

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Thanks for the reply Karl. I wanted to know if the replicates with no data should be removed from the input file or can be used as "NA".

Regards

Laavanya Rayaprolu

Karl Broman

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Sep 6, 2022, 4:22:28 PM9/6/22

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They can be used as “NA”. You should get identical results.

karl

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