[BioC] which statistical test to perform?

[Sean Davis]

On Wed, Nov 23, 2011 at 5:14 AM, anand mt [guest]
<guest at bioconductor.org> wrote:
>
> hi all,
>
> i'm new to this microarray data  analysis.
> recently i've been given data consisting of 11 tissues.
> now i've normalized the data, filtered data using mas5 AP calls. My question is, which statistical test i must perform
> to calculate the significance values ??
>
> sample data is as below:
>
>
>        accumbens       amygdala        cerebellum      corpus.collosum hippocampus     midbrain        p.lobe  putamen s.nigra t.lobe  thalamus
> 1007_s_at       11.93852233     12.21404093     11.46118612     13.41594885     12.42216256     12.89589133     11.58715914     11.85803472     12.79920479     12.07087932     12.55338306
> 1053_at 7.490706858     7.526181155     7.551069308     7.891002293     7.49104271      7.971097552     8.088918072        7.660258014     7.92423132      7.54689645      7.128753703
> 117_at  8.486898268        8.773089087        7.642339349     8.560352732     7.676296801     7.865961146        7.250275943     7.929165261     7.874073766        7.940298941     8.10731601
>
>
> I got some web results, from which i came to know that, chi-square test is of more relevant in this case (to compare 3 or more unmatched groups, binomial). Is it correct to choose chi-square test ??
>
> Sorry if my question is too lame.

Hi, Anand.

I'm assuming that for you the biological question that you are asking
is obvious, but to me it seems unclear.  In particular, what groups
above are you trying to compare?  It seems you have no replicates?

Sean


> thanks in advance.
>
>  -- output of sessionInfo():
>
> R version 2.13.1 (2011-07-08)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] MASS_7.3-13
>
> loaded via a namespace (and not attached):
> [1] tools_2.13.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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