A more general error is that you seem to be doing far more than you need to. Try replacing your first while loop with: 
while($line=<INPUTR>){
    chomp $line;
    my ($freq,$gene) = split(/\t/, $line);
    next if (exists $hashfreq{$gene} and $hashfreq{$gene} >= $freq);
    $hashfreq{$gene} = $freq;
}

[download]
Output: 
20   SEMA4G     20
80   CTBP2      80
80   CTBP2      80
80   CTBP2      80
100  SPRN      100
40   SVIL       40
80   TIMM23     80
80   MINPP1     80
80   BTAF1      80
20   MUC2      100
60   MUC2      100
80   MUC2      100
100  MUC2      100
60   OR10G9     60
60   C11orf91   60
80   OR4S1      80
40   OR4C3      40
40   OR4C3      40
20   OR4C3      40
40   OR4C45     60
60   OR4C45     60

[download]

In reply to Re: Error in Code: Need help by tangent
in thread Error in Code: Need help by angerusso

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