I've formatted my pen drive in FAT format but it's not showing in a Windows laptop, so I'm thinking the formatted pen drive through OS X is not compactible with other OSs. How can I format a pen drive through OS X El Capitan?
OS X and macOS can't format partitions as NTFS or write to NTFS without third-party software (read is built in). Both Windows and Mac support read/write to FAT and you can erase a disk and set the format to FAT in Disk Utility which can be read in Windows. If Windows cannot read the FAT volume then this is a separate problem with the disk or Windows as it should work.
Your flash drive is partitioned using the GUID Partition Table scheme. You need to partition the flash drive using a Master Boot Record scheme. Also you should choose to only have a single partition. You can use either MS-DOS (FAT) or ExFAT formats, but the MS-DOS (FAT) format is more reliable. You do not need to use the ExFAT format unless some files exceed 4 GB in size.
I would advice formatting any drive you want to use between OS X and Windows to exFAT. exFAT supports read/write both on OS X and Windows. You can easily format you drive to exFAT using Disk utility: WD guide and official Apple forum thread.
FAT-32 also works between Mac OS X and Windows just fine, but it limits you to 4GB per-file. exFAT doesn't have such limitation.
In your question you mentioned:
I've formatted my pen drive in FAT format but it's not showing in a Windows laptop
If you want to stick to FAT-32 then try to reformat your drive once again using Disk utility on Mac or format it under Windows. On Windows you might want to uncheck the
Quick format option to ensure better formatting.
Also make sure the USB port you're connecting your drive to is working and the drive itself is not corrupted.