Recently, I got a new CDF file which trimmed some probes out and rearrange probe to probeset. I also got new trimmed probesequence file. I could use new cdf file to generate new cdf envirment and do RMA. I can also generate probe package and install it without any problem. But when I run gcrma, I got the following error message: Error in compute.affinities(cdfName(object), verbose = verbose) : NAs are not allowed in subscripted assignments Anyone know what cause this error and how to solve it? best yan