Thanks a lot for all the responses!!

I then first test my data:

> dim(data)
[1] 52086    13
>  if(grep(data[3,4],data[3,12])==1) print("Y")
[1] "Y"
> for(i in 1:52086){if(grep(data[i,4],data[i,12])==1) print ("Y")}
Error in if (grep(data[i, 4], data[i, 12]) == 1) print("Y") :
  argument is of length zero


What is this new error message? "argument is of length zero"

Here is my data format:
>head(data)

           V1     V2         V3           V4       V5  V6       V7           V8
1 ref_gene_id ref_id class_code cuff_gene_id  cuff_id FMI     FPKM FPKM_conf_lo
2           -      -          u       C.3 C.3.1 100 1.000000     0.000000
3           -      -          u       C.2 C.2.1 100 1.000000     0.000000
4           -      -          u       C.4 C.4.1 100 1.000000     0.000000
5           -      -          u       C.1 C.1.1 100 1.000000     0.000000
6           -      -          u       C.5 C.5.1 100 1.000000     0.000000
            V9      V10 V11          V12           V13
1 FPKM_conf_hi      cov len major_iso_id ref_match_len
2     0.000000 0.056682  96     C.3.1             -
3     0.000000 0.058453  99     C.2.1             -
4     0.000000 0.059634 101     C.4.1             -
5     0.000000 0.059634 101     C.2.1             -
6     0.000000 0.059634 101     C.5.1             -


________________________________
 From: Jeff Newmiller <jdnewmil@dcn.davis.CA.us>

help@r-project.org" <r-help@r-project.org> 
Sent: Friday, September 13, 2013 9:21 PM
Subject: Re: [R] problem with grep under loop


This is because you are not printing it (with the print or cat functions). Keep in mind that the visible result you get from calling a function or evaluating a variable interactively comes from the interactive R command line, not from R itself. Once you put such an expression inside a function (such as the "for" function) it is no longer directly being invoked by the command interpreter.

You might want to read [1] and [2] (which says don't post using HTML).

[1] http://stackoverflow.com/questions/4716152/why-do-r-objects-not-print-in-a-function-or-a-for-loop
[2] http://www.R-project.org/posting-guide.html
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>
>
>I am just testing the possibility of using grep under for loop:
>
>>for(i in 1:10){grep("a",letters)}
>
>
>nothing came out;
>
>when I ran: 
>
>
>>grep("a",letters), 
>
>
>I got "1"
>
>so in my for loop, I expected to see ten "1"s, but I did not.
>
>Could anybody help me to figure out why? Thanks a lot for your help.
>
>Capricy
>    [[alternative HTML version deleted]]
>
>______________________________________________
>R-help@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
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