Hi Kevin This was super helpful! I learned a lot about this. I am new to heritability but this was a great resource to learn. I have a question about your model. Did you ever encounter and error like this: 'Error: number of levels of each grouping factor must be < number of observations' I mean I think I know why because the data I am using is from a p-rep design so there is variation in the reps of the entries so maybe this is effecting the model. There is a temp solution but I don't really like it because all of the variance values become the same. With your data did all of your entries have the same # reps?
Thanks for the useful video. I am wondering about the model, I have two-year data of a single location, and the RCBD design was used (replicated three times, and 10 plants were taken from each genotype). So, which model I should use? BLUE or BLUP? And how I should calculate the Heritability? Later, I wanted to do SNP-GWAS. Thanks!
Hi Kevin, very helpfull tutorial, thanks a bunch! Question: In your experimental design you have 12 (or 14?) reps (one in every subblock) if I understood you well, so you set your nloc to "14". My data is not balanced, I have more replications for some genotypes and less for others, I am a bit uncertain if I shood set nloc to anything... If I do not use nloc (i.e. set it to 1) my heritability becomes rather low. What would your advice be?
Hi Kevin. Thank you for your tutorial, it has been really interesting. I am getting into BLUPs analyses and heritability estimates for cold hardiness in polyploid roses. I am working at the moment with only two environments so I am thinking setting environment as a fixed effect and genotype as a random effect. My response variable is a ratio of two stem measurements taken in the field. I was wondering if you had any experience or suggestion on modelling proportion data with lme4 specifying a beta distribution. Thank you.
Hi Cindy. Thank you for your kind words. Interesting question. In my experience I have yet to work with a beta distribution however, Sarah is working with nematode counts with a similar distribution issue. I will look deeper into this.
I appreciate the very helpful video! I was wondering, what is "Entry" in df? Is it a unique plant identifier or do all 12 reps within each genotype share the same Entry number? Maybe I'm completely off.
My experimental design was essentially a RCBD using 12 growth chambers (which I call sub-blocks in the video but are essentially reps) and 292 genotypes (of which 12 plants were grown of each).
The heritability estimates seems to be too high. Can you please conform if the equation you used is the correct one. I have similar root traits (total length, primary root length, lateral root length) and trying to calculate heritability. Are there any other models or equations used for heritability calculation.
@@KevinFalk Dear Mr. Kevin.. if you mind could you share a date set as an example..? maybe this very helpfull to me to learning step by step.. many thank & God bless you
Thank you for your nice sharing. Sorry, I tried to get to your github, but could not find the data file (.csv), Can you share your data file? Thank you.
I cannot share this data file. However, there is a sample data file in my Github located here: /mighster/ARIA2.0/blob/master/05-07-2019_KGF_RawData_iRootonly.csv
Thanks kevin bro,
It was really helpful me. As a beginner I was able to calculate blups from augmented design
Hi Kevin
This was super helpful! I learned a lot about this. I am new to heritability but this was a great resource to learn. I have a question about your model. Did you ever encounter and error like this: 'Error: number of levels of each grouping factor must be < number of observations'
I mean I think I know why because the data I am using is from a p-rep design so there is variation in the reps of the entries so maybe this is effecting the model. There is a temp solution but I don't really like it because all of the variance values become the same. With your data did all of your entries have the same # reps?
Thanks for the useful video. I am wondering about the model, I have two-year data of a single location, and the RCBD design was used (replicated three times, and 10 plants were taken from each genotype). So, which model I should use? BLUE or BLUP? And how I should calculate the Heritability? Later, I wanted to do SNP-GWAS. Thanks!
Hi Kevin, very helpfull tutorial, thanks a bunch!
Question: In your experimental design you have 12 (or 14?) reps (one in every subblock) if I understood you well, so you set your nloc to "14". My data is not balanced, I have more replications for some genotypes and less for others, I am a bit uncertain if I shood set nloc to anything... If I do not use nloc (i.e. set it to 1) my heritability becomes rather low. What would your advice be?
thanks!
can we estimate different type of blup? for example Blup broad , Blup Narrow and Blup intermediate
Thank for the video and could you please share me the soft copy of the book you recommended.
Hi Kevin. Thank you for your tutorial, it has been really interesting. I am getting into BLUPs analyses and heritability estimates for cold hardiness in polyploid roses. I am working at the moment with only two environments so I am thinking setting environment as a fixed effect and genotype as a random effect. My response variable is a ratio of two stem measurements taken in the field. I was wondering if you had any experience or suggestion on modelling proportion data with lme4 specifying a beta distribution. Thank you.
Hi Cindy. Thank you for your kind words. Interesting question. In my experience I have yet to work with a beta distribution however, Sarah is working with nematode counts with a similar distribution issue. I will look deeper into this.
@@KevinFalk Thanks a lot!
Interesting
Can I use the same to proceedure in animals without having parents information apart from identity of dams and sires?
hello kevin... please share with me the phenotypinc dataframe to know for stepwise analysis
I appreciate the very helpful video! I was wondering, what is "Entry" in df? Is it a unique plant identifier or do all 12 reps within each genotype share the same Entry number? Maybe I'm completely off.
Entry is the genotype. It will appear in each replicate.
@@KevinFalk Thank you!
Hi, Kevin, I am curious your experimental design? Could you explain a little bit of your design, which concerns the linear model.
My experimental design was essentially a RCBD using 12 growth chambers (which I call sub-blocks in the video but are essentially reps) and 292 genotypes (of which 12 plants were grown of each).
@@KevinFalk Another question, did do the ANOVA test to check what's factors(like, Subplot) are significant or not then put then in BLUP ?
@@jizhogjie1205 yes I did do that
The heritability estimates seems to be too high. Can you please conform if the equation you used is the correct one. I have similar root traits (total length, primary root length, lateral root length) and trying to calculate heritability. Are there any other models or equations used for heritability calculation.
I think that formula is for narrow sense heritability instead of broad sense as he is not including variance of residuals.
Sir
Please provide the methodology for estimation of Pedigree Matrix from Coefficient of Coancestry
regards
mahadev
Hi Kevin.. have you any suggest others book have already discuss about your topic? And thank for your attention
I recommend Breeding for Quantitative Traits in Plants by Rex Bernardo.
@@KevinFalk Dear Mr. Kevin.. if you mind could you share a date set as an example..? maybe this very helpfull to me to learning step by step.. many thank & God bless you
Thank you for your nice sharing. Sorry, I tried to get to your github, but could not find the data file (.csv), Can you share your data file? Thank you.
I cannot share this data file. However, there is a sample data file in my Github located here: /mighster/ARIA2.0/blob/master/05-07-2019_KGF_RawData_iRootonly.csv
@@KevinFalk Thank you for your prompt reply. I'm also doing phD in root system traits in soybean (GWAS) and this is very helpful.
hello you got data file CSV
if u means please share with me
hi Kevin, my name rizki and I'm oil palm breeder, can I see your data frame ? thank you very much,
Hi Rizki. My code and data files are on my Github page, link in the description.