Predict the random effects by BLUP

ab99
New Member

Posts: 8

Predict the random effects by BLUP Sept 10, 2014 14:57:39 GMT

Quote

Post by ab99 on Sept 10, 2014 14:57:39 GMT

Dear All,

I am using the "--reml-pred-rand" option to predict the random effects by the BLUP method. I am not sure if I completely understand this method correctly. I have the following two questions:

1) Based on the manual, the output file "*.indi.blp" will output two columns for each GRM matrix: an intermediate variable, and the total genetic effect. Can somebody explain what this "intermediate variable" is? I am guessing what we care about is the "total genetic effect" column, so can I completely ignore the "intermediate variable" column?

2) Is it meaningful to calculate the correlation (or more precisely, the correlation square) between the observed phenotype and the "total genetic effect" column? I am thinking this would be the R2 between the observed phenotype and the predicted genetic effect, so it should be <= the total variance explained by all the SNPs (i.e., V_G/V_p), which is the main result from GCTA. Is this right?

Thank you very much!
ab99

Zhihong Zhu Moderator Posts: 88	Predict the random effects by BLUP Sept 11, 2014 6:41:27 GMT ab99 likes this Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by Zhihong Zhu on Sept 11, 2014 6:41:27 GMT Re 1) Yes. Re 2) Yes, the R^2 will be similar to hg^2 in .hsq file. But SE, which is important, is unable to obtain from that.

ab99
New Member

Posts: 8

Predict the random effects by BLUP Sept 11, 2014 15:30:05 GMT

Quote

Post by ab99 on Sept 11, 2014 15:30:05 GMT

Sept 11, 2014 6:41:27 GMT Zhihong Zhu said:

Re 1) Yes.
Re 2) Yes, the R^2 will be similar to hg^2 in .hsq file. But SE, which is important, is unable to obtain from that.

Hi Zhihong,

Thank you for your reply!

Just a follow-up with 2): what you said was what I originally thought. However, we've looked at 5 quantitative traits, among which 4 has R^2 (calculated as I mentioned in my original thread) significantly larger than hg^2 (i.e., V_G/V_p) in .hsq files. This does not make sense to us. Do you have any thoughts on this?

Also, I appreciate if you can explain a bit what the "intermediate variable" is in the .indi.blp files.

Thanks,
ab99

Jian Yang
Administrator

Posts: 362

Predict the random effects by BLUP Sept 12, 2014 9:52:46 GMT

Quote

Post by Jian Yang on Sept 12, 2014 9:52:46 GMT

Re 1) The prediction analysis needs to be done in an independent sample, i.e. using the SNP BLUP effects to compute a predictor of in a new sample.

Re 2) "intermediate variable". You can ignore this. It is only used to compute SNP BLUP.

ab99
New Member

Posts: 8

Predict the random effects by BLUP Sept 16, 2014 2:52:21 GMT

Quote

Post by ab99 on Sept 16, 2014 2:52:21 GMT

Sept 12, 2014 9:52:46 GMT Jian Yang said:

Re 1) The prediction analysis needs to be done in an independent sample, i.e. using the SNP BLUP effects to compute a predictor of in a new sample.

Re 2) "intermediate variable". You can ignore this. It is only used to compute SNP BLUP.

Hi Jian,

Thank you very much for your reply!

I understand that the prediction analysis is better to be done in an independent sample. But my question is if I do want to get a predicted phenotype in the original data set (i.e. get the y_hat), can I do that? Specifically, can I use 1) the "total genetic effect", or 2) the original phenotype minus "residual effect" as the predicted phenotype?

I may be completely wrong about this, but I do hope to get an answer from you. Thank you again!
ab99

NR
Guest

Predict the random effects by BLUP Sept 30, 2014 9:53:21 GMT

Quote

Post by NR on Sept 30, 2014 9:53:21 GMT

Hi Jian and ab99,

I did the same observation: when I calculated the BLUP in the GREML analysis sample, the explained variance is much higher than the SNP-heritability. I don't understand this, because it should be the same? (if I understand Chapter 26 of Lynch & Walsh correctly). It does not happen with all phenotypes. For height I get more or less the same amount of explained variance.

Thanks!

Post by ab99 on Sept 10, 2014 14:57:39 GMT

Post by Zhihong Zhu on Sept 11, 2014 6:41:27 GMT

Post by ab99 on Sept 11, 2014 15:30:05 GMT

Post by Jian Yang on Sept 12, 2014 9:52:46 GMT

Post by ab99 on Sept 16, 2014 2:52:21 GMT

Post by NR on Sept 30, 2014 9:53:21 GMT