Maybe I'm confused about what you're trying to do. I assumed that your file3.txt on is something like:

Code:

Gene exp1 exp2 exp3 exp4 exp5
ABC 2 3 4 5 7
MNO 5.5 6.8 7.6 5.5 4.2
DEF 1 4 6 7 9
GHI 3 5 6 7 8 0 
LMN 2.2 3.4 5.7 8.9 7.2
TQR 4 5 6 8 8

and that the contents of file3 you showed us in the 1st message in this thread was the desired output. You could do that with something like:

Code:

awk '
FNR == 1 {
	if(++f > 2) print $0, "enriched", "repressed"
	next
}
f < 3 {	gene[f,$1]
	next
}
{	print $0, (1,$1) in gene ? "yes" : "no", (2,$1) in gene ? "yes" : "no"
}' file[1-3].txt

The test in your code:

Code:

 if ($0 ~ key)

would never match. For example, on the 1st data line in file3.txt when key is ABC, the test would expand to:

Code:

if ("ABC 2 3 4 5 7" ~ "ABC")

Perhaps you meant:

Code:

if ($1 == key)

But, I thought you were trying to add two columns of "yes" or "no" to the contents of file3.txt at the end of the lines. Instead you're adding the string "file3.txt" to the start of a line from file3.txt???

Please explain more clearly what file3.txt is on input and exactly what output you want to produce.