When deploying IBM iSeries Access for Windows, you can use the included setup.ini file to specify standard MSI command-line switches to be used.  The line is located under the [Startup] section and called CmdLine.

For example, to write a log to the C:\Logs folder, replace what is there with:
CmdLine=/l "C:\Logs\IBM_iSeries_Access.log"

To choose which features to install, use the standard ADDLOCAL= switch with one or more of the following (separated by commas):

Feature                      Internal name of feature
Required Programs            req
Directory Update             dir
Incoming Remote Command      irc
Data Transfer                dt
Data Transfer Excel Add-in   dtexcel
ODBC                         odbc
OLE DB Provider              oledb
Lotus® 123 File Format Support  lotus123
.NET Data Provider           dotnet
AFP Workbench Viewer         viewer
5250 Display and Printer Emulator  emu
Secure Socket Layer (SSL)    ssl
AFP Printer Driver           afp
SCS Printer Driver           scs
Operations Console           oc
Headers, Libraries, and Documentation   hld
System i® Navigator (Base Support)   inav
Basic Operatons              inavbo
Work Management              inavwm
Configuration and Services   inavcfg
Networks                     inavnet
Integrated Server Administration   inavisa
Security                     inavsec
Users and Groups             inavug
Databases                    inavdb
File Systems                 inavfs
Backup                       inavback
Commands                     inavcmd
Packages and Products        inavpp
Monitors                     inavmon
Logical Systems              inavlog
AFP Manager                  inavafp
Application Administration   inavad
Toolbox for Java             tbj
Java™ Programmer's Tools     jpt

For example, to install only the required files and the "5250 Display and Print Emulator" along with a verbose log, no reboot, and silently with no user interface, the line would look like this:
CmdLine=/l*v "c:\Logs\IBM_iSeries_Access.log" ADDLOCAL=req,emu REBOOT=ReallySupress /qn

When calling the setup.exe from a command-line, deployment tool or script, it should be called with a /S switch.

You can also pass standard MSI command-line switches to the setup.exe directly, using the /v switch.

Ex: setup.exe /v"/l*v C:\Logs\IBM_iSeries_Access.log" /vADDLOCAL=req,emu /vREBOOT=ReallySupress