Dear Kuldeep Kumar;

when you are plotting if all the values ​​in y or x are NAs, you will get this error. Just remove the columns or rows that are entirely NA's.

Goodluck

Madam, Peymaneh Davoodi Peymaneh Davoodi

As you mentioned, I have checked about the x or Y axis column containing entirely NAs, but n such rows or column are found in my hapmap file, except the default columns like, "assembly", "center", "protLSID", "assayLSID", "panel", "Qccode". shall I remove them or any other solution. I have attached a snap of my file

Hi Kuldeep Kumar

It is quite clear that the last three columns in your Hopmap data file are filled with NA. Although I have worked with numerical formats using GAPIT. I have no idea whether you need the information on those last three columns ( "assayLSID", "panel", "Qccode"), but if they are not informative, I suggest you delete them and run the GAPIT.

You had better keep the original file and make a copy to check what is going to happen by removing the mentioned columns.

Best Regards

Madam @Peymaneh Davoodi, I already have tried what you have suggested but the error is persistent. The thing is same hapmap file works well for quantitative trait, but not for qualitative.

Hello again

So it should definitely be related to the phenotypic data structure, whether the NAs in your data file or their assigned values: something related to coding them.