Hi all,

I have the following dataset:

```
ï..TGEClass.known TGEClass.uknown
1 GVVEVTHDLQK GVVEVTHDLQK
2 LFYADHPFIFLVR LFYADHPFIFLVR
3 SALQSINEWAAQTTDGK SALQSINEWAAQTTDGK
4 AVLSAEQLRDEEVHAGLGELLR AVLSAEQLRDEEVHAGLGELL
```

I would like to calculate please the number of peptides that are present in both categories and those that are not.

I have tried to use the Venn count function from limma but that only accepts numerical values:

```
a <- vennCounts(c3)
a
hw hm hr Counts
[1,] 0 0 0 113
[2,] 0 0 1 18
[3,] 0 1 0 8
[4,] 0 1 1 8
[5,] 1 0 0 12
[6,] 1 0 1 8
[7,] 1 1 0 11
[8,] 1 1 1 22
```

How I can convert my peptide dataset like that dataset above so that I can make a Venn diagram. I have researched everywhere I can but still failed to find the solution.

I would really appreciate it if someone could help me solve this problem.

Many Thanks,

Ishack

Hi SMK, Thanks very much for your answer but how can I get a table like this automatically, it is quite long to do it manually?

What are

`hw`

,`hm`

, and`hr`

?Sorry those are meant to say TGEClass.uknown and TGEClass known. Please ignore the hw, hm and hr, I want table like that for TGEClass known and TGEClass unknown

Perhaps:

Hi SMK thanks a lot thats what was look for. Just one final question if you don't mind.

I have a lot of data frames like the one above but each one has a different number of categories and also different categories, would it be possible to intersect and setdif between all the different columns automatically?

Got an idea from the function:

`venn`

, here demonstrating 2 sets and 3 sets:Hi SMK, Unfortunately, I found just now that I can't do a Venn diagram for more than 5 categories.

Can you help me create a df that looks like this please?

Thanks very much

Hi SMK,

Thanks very much for your quick response, I have been trying all day to fix this. You are a life saver!

Hi SMK, sorry for the lateness, is there a way to see the number of unique peptides from each category when there are blanks in columns, please?

the

`length code`

sees the blank cells as unique peptides, unfortunately.Hi ishackm,

You can remove the empty element in list before you use

`venn`

:Hi SMK , thank you again for your quick response. Much Appreciated.

Cool, glad it helps!