[BioC] Very Different group sizes in DE of two conditions

[Gordon K Smyth]

> Date: Tue,  3 Jul 2012 03:08:25 -0700 (PDT)
> From: "Moriah [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, moriahcohen at gmail.com
> Subject: [BioC] Very Different group sizes in  DE of two conditions
>
> Hi,
>
> I would like to conduct DE analysis of miRNA and mRNA using DESeq and 
> EdgeR on two conditions (Breast cancer subtypes) the problem is that for 
> one condition I have 122 samples and for the second only 22.  I would 
> like to know if it is O.K to run DE on such different size groups ?

Yes, it is no problem whatsoever.

Gordon

> What I tried to do is to run 100 different permutations of 22 samples 
> out of 122 and to try to run DE and search for differentially expressed 
> miRNA in all 100 different permutations against the 22 from the second 
> condition.
>
> I got only one miRNA that is differentially expressed in DESeq in all 
> permutaions but when I run 122 samples against 22 samples I got no such 
> miRNA. There is a difference between EdgeR results as well.
>
> Is my way of creating samller groups is applicable? Or is there any 
> other way to deal with such different group sizes?
>
> Thanks!
>
> -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C
> [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] edgeR_2.6.7    limma_3.12.1   DESeq_1.8.3    locfit_1.5-8   Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] annotate_1.34.0      AnnotationDbi_1.18.1 BiocGenerics_0.2.0
> [4] DBI_0.2-5            genefilter_1.38.0    geneplotter_1.34.0
> [7] grid_2.15.1          IRanges_1.14.3       lattice_0.20-6
> [10] RColorBrewer_1.0-5   RSQLite_0.11.1       splines_2.15.1
> [13] stats4_2.15.1        survival_2.36-14     xtable_1.7-0
>>

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