Moved this to an answer.
As per Inquisitive8995, you can remove samples within PLINK, and this is the safest place to do this unless you really have a firm understanding of how PLINK arranges data. Please spend some time looking through the documentation.
Phenotype (case/control) and gender (sex) information, if they exist, would be stored in the FAM and/or the first few columns of the PED file. Again, check the documentation to ensure that you know to which column each relates.
For mapping your Affymetrix IDs to rs IDs, you will have a difficult task. Probably the easiest way is to use the chr and base position information from your MAP file to map each to a rs ID. You can then either leave the Affymetrix IDs as they currently are and map to rs IDs when you generate your final results, or attempt to update the IDs within the PLINK objects (check the documentation).
You can download the annotation file for your array from the Affymetrix / ThermoFisher web-site and see if that contains rs ID, which can then be mapped back to probe ID.
maybe slightly off topic but if you are new to GWAS and Affy you may wish to take note of this http://www.affymetrix.com/support/help/faqs/dna_ge_arrays/faq_32.jsp
Many thanks all, your tips were useful, wonderful!! Now, I have other question about this error:
A problem with line 124 in [ C:\Users\leka_\Documents\DOUTORADO\gwas\gwas\Dataset\gwas_26032019\plink_text_format\JSB_AX001toAX011_final.ped ] Expecting 6 + 2 * 920636 = 1841278 columns, but found 1455707
When I'm try to remove this individual( line 124). I can not! How I can to solve this problem? Because any analysis running not is working.
Many thanks!!
Your PED file is essentially not in agreement with [most likely] your MAP file.
The PED file has 6 columns for:
Then, the remaining columns are genotype values, with 2 columns per genotype (so, 2 * the number of genotypes)