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How to change IEEEtran \IEEEauthorrefmark to numbered style 1, 2, 3... instead of the star and dagger marks and make the author affiliation as footnote in the first page?

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For the first question, you need to completely redefine \IEEEauthorrefmark:

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It's not working! – sajjadG Sep 23 '13 at 12:20
@sajjadG: There was a strange character caught in the command above. Copy-and-paste and try again. – Werner Sep 23 '13 at 14:08

You can discard \IEEEauthorrefmark{} and use simple upperscript for this purpose. something like this:

\IEEEauthorblockN {
   Author1$^{a,b}$,       %%% instead of \IEEEauthorrefmark{1},
   Author2$^{a,b}$       %%% instead of \IEEEauthorrefmark{1}
   and Author3$^{a,c}$ %%% instead of \IEEEauthorrefmark{1}\IEEEauthorrefmark{4}

\IEEEauthorblockA {
  $^{a}$Department  of Mathematics and Computer Science\\
  silent hill University\\
  City, Country \\
\IEEEauthorblockA {
    %%% \IEEEauthorrefmark{4}%\IEEEauthorrefmark{2}
}%%% author
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If this is going to be submitted to IEEE, don't alter them. It will be recorrected by the publication office. – percusse Sep 23 '13 at 13:46
@percusse It seems that some of the IEEE conferences don't! I got an Email from the Conference that asks me to edit the note marks and send them the edited version! I didn't get them my latex file! they asked for just word version and I didn't have one! so I emailed them and said that I don't have a doc file but I have a latex file that uses IEEE trans class and is compatible to IEEE conf. standards. they didn't answered me! My paper accepted and know they send me email for correction! – sajjadG Sep 23 '13 at 13:55
for conferences you don't need to use any marks. The conference template has been changed but nobody cares. I use ieeeconf and nobody has been complaining so far. – percusse Sep 23 '13 at 13:56
@percusse IEEE conference templates has been changed? when? I got the template from their site lately, about 2-3 month ago I think. First they offered word and latex template. I used latex and wrote my paper. then they posted and said that you should use this new template if you want your paper to be indexed by IEEE and They just provide a word template and I had to create my own latex template (because I hate M$ word and my paper was in latex and converting to word was hard). I emailed them that I made a latex template same as your word version and I checked IEEE latex template. whole story! – sajjadG Sep 23 '13 at 14:06
The official story is more complicated but conferences stopped using conference mode of the ieeetran template. So in the paperplaza or manuscript central often organizers provide the custom templates of ieeeconf but there is no consensus. If they don't even have a latex template just send them default ieeeconf and complain if they want to change it. – percusse Sep 23 '13 at 14:21

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