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Old 10-03-2011, 11:57 AM   #3
byou678
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Location: Maryland

Join Date: Aug 2011
Posts: 52
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Thanks ECO, I run the similar codes in R, too. And I can get the result like yours Just based on the Spreadsheets showed in this thread. Sorry for not telling more info about my data:But I have more Genes(37970) in Spreadsheet2 than Spreadsheet1 (17980). It supposed to have 17980 Genes left after merging [the 19990(37970-17980) Genes which only in Spreadsheet2 will not appear in the merged sheets]. Unfortunately, it messed up after merging. Any idea will be greatly appreciated.

Quote:
Originally Posted by ECO View Post
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

Last edited by byou678; 10-03-2011 at 12:08 PM.
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