[BioC] identifying consistently expressed genes between replicates

[Gordon K Smyth]

Dear Wendy,

>From your email, I assume that you have found signature genes by comparing 
each cell type to all the other cell types treated as one group.  As you 
have correctly observed, this does not take account of consistency within 
the other cell types.  Another way to find signature genes, that I think 
is superior, is to choose signature genes to be those genes that are 
uniquely higher or lower in the relevant cell type with respect to each of 
the other cell types individually.  In other words, a positive signature 
gene is higher in the relevant cell type against every other cell type, 
not just against the average of the other cell types.  This was the method 
used in:

Lim E, Vaillant F, Wu D, Forrest NC, Pal B, Hart AH, Asselin-Labat ML, 
Gyorki DE, Ward T, Partanen A, Feleppa F, Huschtscha LI, Thorne HJ; 
kConFab, Fox SB, Yan M, French JD, Brown MA, Smyth GK, Visvader JE, 
Lindeman GJ.
Aberrant luminal progenitors as the candidate target population for basal 
tumor development in BRCA1 mutation carriers.  Nature Medicine 2009.

to find stem cell signature genes.  If you do it this way, consistency 
within the cell types is automatically taken care off, because the t-tests 
will only choose genes with consistent behaviour.   limma can do all the 
relevant pairwise tests for you in a couple of lines, then use 
decideTests() to choose the signature genes.

Best wishes
Gordon

---------------------------------------------
Professor Gordon K Smyth,
NHMRC Senior Research Fellow,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Tel: (03) 9345 2326, Fax (03) 9347 0852,
smyth at wehi.edu.au
http://www.wehi.edu.au
http://www.statsci.org/smyth


> Date: Sat, 9 Apr 2011 19:57:25 -0400
> From: Wendy Qiao <wendy2.qiao at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] identifying consistently expressed genes between
> 	replicates
>
> Hi all,
>
> I am comparing a number of cell types, and am wanting to find the signature
> genes of each cell type. I used the limma package to do this. The signature
> genes of a given cell type are found by the fold different between the given
> cell type and grand mean of all the cell types, as well as the BH-adjusted
> p-values. I want to add another condition to test the consistency of
> expression levels of the selected genes for each cell type. I can do this by
> looking at the standard deviations of gene expressions between replicates. I
> am just wondering if there is any function in limma or other BioConductor
> package to do this.
>
> Thank you in advance,
> Wendy

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