p.s: since the "data" (Y variable) is very much not normal (also after a log
transform)I would consider going with an a-parametric test
check:
? wilcox.test
(for a non parametric t.test )
OR
(for a non parametric simple anova)
?kruskal.test




On Sat, Mar 7, 2009 at 11:51 PM, Tal Galili <tal.galili@gmail.com> wrote:

> Hello friend.
>
> I believe anova might be a better solution for you.
> You might have a look here:
> http://www.personality-project.org/r/r.anova.html
>
> A simple R session that will work for you is:
>
> # getting the data in:
> data1 <- read.table( "enter the path of the file here, look at  ?read.table
> for exact syntax)
>
> aov1 <- aov(data ~ gender +  disease + genotype       ,data = data1)
> summary(aov1)
>
>
> If you insist on t.test, here is the way:
> t.test(data ~ gender       ,data = data1)
> t.test(data ~ disease       ,data = data1)
> t.test(data ~ genotype       ,data = data1)
>
>
> Cheers,
> Tal
>
>
>
>
> On Sat, Mar 7, 2009 at 9:23 PM, 1Rnwb <sbpurohit@gmail.com> wrote:
>
>>
>> Dear list,
>>
>> i am a biologist who needs to do some ttest between disease and non
>> disease,
>> sex, genotype and the serum levels of proteins on a large number of
>> individuals. i have been using excel for a long time but it is very
>> tedious
>> and time consuming. i am posting the data below and ask your help in
>> generating a code to get this analysis done in R. thanks
>>
>> gender  disease genotype        data
>> M       N       CC      3.206447188
>> F       N       CC      8.2
>> M       N       CC      15.78908629
>> M       N       CC      21.14311843
>> F       N       CC      21.48413647
>> M       N       CC      30.08028842
>> M       N       CC      30.11455009
>> F       N       CC      32.41258845
>> F       N       CT      6622.253065
>> M       N       CT      6763.6
>> M       N       CT      7342.023209
>> F       N       CT      7617.7
>> F       N       CT      7857.3
>> M       N       CT      8027.78692
>> F       N       CT      8755.950438
>> M       N       CT      9007.7
>> F       N       CT      9157.76987
>> M       N       CT      9398.270953
>> F       N       CT      9710.083037
>> F       N       CT      9896.887277
>> M       N       CT      10082.60082
>> F       N       CT      10137.05244
>> F       N       CT      10350.76186
>> M       N       CT      14629.34508
>> F       N       TT      4.614829254
>> F       N       TT      5.223593964
>> F       N       TT      6.7
>> M       N       TT      6.7
>> M       N       TT      7.735287229
>> F       N       TT      13.68084134
>> F       N       TT      14.5
>> M       N       TT      15.3
>> M       N       TT      16.16826703
>> M       N       TT      19.8
>> M       N       TT      24.51271254
>> M       N       TT      29.92459383
>> F       N       TT      30.3993842
>> M       N       TT      30.57161207
>> F       N       TT      30.72031553
>> F       N       TT      31.8
>> F       N       TT      34.72409961
>> M       N       TT      37
>> F       N       TT      38.94507607
>> M       N       TT      39.1
>> M       N       TT      40.9
>> M       N       TT      41.5
>> F       N       TT      42.36614019
>> F       Y       CC      338.2166757
>> M       Y       CC      345.8711007
>> M       Y       CC      347.4659528
>> F       Y       CC      356.3
>> F       Y       CC      358.4
>> F       Y       CC      360.184259
>> F       Y       CC      453.8
>> F       Y       CC      573.7342373
>> M       Y       CC      962.1232959
>> F       Y       CC      1055.9
>> F       Y       CC      1309.532621
>> F       Y       CC      2798.6
>> F       Y       CC      3568.794326
>> M       Y       CT      1.227348206
>> F       Y       CT      2.061944986
>> F       Y       CT      2.245592643
>> M       Y       CT      2.454696412
>> M       Y       CT      2.456716738
>> M       Y       CT      4.318447391
>> M       Y       CT      4.503098245
>> M       Y       CT      5.873088452
>> M       Y       CT      7.106930564
>> F       Y       CT      7.7
>> M       Y       CT      10.83537709
>> M       Y       CT      11.4
>> M       Y       CT      12.1
>> M       Y       CT      12.62002743
>> M       Y       CT      13.6
>> F       Y       CT      13.7
>> F       Y       CT      14.35562171
>> F       Y       CT      15.9
>> F       Y       TT      986.6755719
>> F       Y       TT      1206.475083
>> F       Y       TT      1237.9
>> M       Y       TT      1254.5
>> F       Y       TT      1303.6
>> F       Y       TT      1573.915019
>> M       Y       TT      1756.8
>> M       Y       TT      1895
>> M       Y       TT      2126.766565
>> F       Y       TT      2149.512866
>> M       Y       TT      3249.449945
>> F       Y       TT      6999.3
>> M       Y       TT      7172.479241
>> M       Y       TT      8268.909251
>> M       Y       TT      8544.229671
>>
>> --
>> View this message in context:
>> http://www.nabble.com/ttest-in-R-tp22390889p22390889.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> ______________________________________________
>> 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.
>>
>
>
>
> --
> ----------------------------------------------
>
>
> My contact information:
> Tal Galili
> Phone number: 972-50-3373767
> FaceBook: Tal Galili
> My Blogs:
> www.talgalili.com
> www.biostatistics.co.il
>
>
>


-- 
----------------------------------------------


My contact information:
Tal Galili
Phone number: 972-50-3373767
FaceBook: Tal Galili
My Blogs:
www.talgalili.com
www.biostatistics.co.il

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