This is cake in R...
Depending on how large the datasets are, read them into R. The example below (using read.table) is just for using the clipboard in MacOSX (highlight in excel, copy, then run that line). The equiv in windows is read.table("clipboard",sep='\t',header=TRUE).
Code:
> df1 <- read.table(pipe("pbpaste"),header=TRUE)
> df1
Gene Change Padj
1 1 212 0.00060
2 2 99 0.09000
3 3 15 0.70000
4 4 59 0.45600
5 5 418 0.00001
6 6 566 0.00000
> df2 <- read.table(pipe("pbpaste"),header=TRUE)
> df2
Gene Statistic FDR
1 1 28 0.0005
2 2 17 0.0070
3 3 3 0.8100
4 4 8 0.2800
5 5 48 0.0020
6 6 111 0.0000
> df3 <- merge(df1,df2)
> df3
Gene Change Padj Statistic FDR
1 1 212 0.00060 28 0.0005
2 2 99 0.09000 17 0.0070
3 3 15 0.70000 3 0.8100
4 4 59 0.45600 8 0.2800
5 5 418 0.00001 48 0.0020
6 6 566 0.00000 111 0.0000
> df3[df3$Padj< 0.05 & df3$FDR < 0.05,]
Gene Change Padj Statistic FDR
1 1 212 6e-04 28 5e-04
5 5 418 1e-05 48 2e-03
6 6 566 0e+00 111 0e+00
> write.csv(df3[df3$Padj< 0.05 & df3$FDR < 0.05,])
"","Gene","Change","Padj","Statistic","FDR"
"1",1,212,6e-04,28,5e-04
"5",5,418,1e-05,48,0.002
"6",6,566,0,111,0