Try this, instead of the trim
aqConvert.VarToInt(Aliases.iexplore1_new.Page.SampleDetails.Panel(2).Panel(0).Panel(0).Panel(0).Panel(21).Panel(0).Panel(80).innerText)
However, I would recommend actually you do something more on the lines of
if (!(aqConvert.VarToStr(baselinevalue) == aqString.Trim(Aliases.iexplore1_new.Page.SampleDetails.Panel(2).Panel(0).Panel(0).Panel(0).Panel(21).Panel(0).Panel(80).innerText, aqString.stAll))
As mentioned above, I think the problem you're having is related to the fact that the innerText value is a string but it's possible that your baseline value is actually numeric and so the conversion of one to the other is not playing nice. A more explicit conversion might work better.