BC dataset

Search capecitabine  in GEO

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22358

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18728

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23988

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20271

capecitabine -- metabolic

http://www.medscape.com/viewarticle/712105

The study authors found that the addition of capecitabine seemed more effective in estrogen-receptor (ER)-positive than in ER-negative breast cancers, Dr. O'Regan points out.

"The positive findings in the capecitabine group could be explained by the fact that over three quarters of patients had ER-positive cancers," she writes. "There is currently no plausible mechanism to explain why capecitabine would be more effective in ER-positive disease, but this might warrant further study."

Capecitabine in advanced breast cancer: Predictive factors for response.

http://www.asco.org/ascov2/Meetings/Abstracts?&vmview=abst_detail_view&confID=55&abstractID=31750

The only positive correlation to predict response was ER positivity (p = 0.04).

http://www.ncbi.nlm.nih.gov/pubmed/18765464

Thymidine phosphorylase expression and benefit from capecitabine in patients with advanced breast cancer.

www.r-tutor.com

http://www.r-tutor.com/elementary-statistics/non-parametric-methods/kruskal-wallis-test

http://www.ihcworld.com/_books/books.htm

http://www.ihcworld.com/_books/books.htm

limma anova

http://www.statsci.org/smyth/pubs/limma-biocbook-reprint.pdf

http://bioconductor.org/packages/2.6/bioc/vignettes/limma/inst/doc/usersguide.pdf

https://stat.ethz.ch/pipermail/bioconductor/2006-August/013998.html

http://www.bioconductor.org/help/course-materials/2009/BioC2009/labs/limma/limma.pdf

KO <- factor(rep(1:2, each = 3, times = 2))
CELL <- factor(rep(1:2, each = 6))
design <- model.matrix(~KO + CELL)




In R:
> mat <- cbind(c(1,1,1,rep(0,9)),
+ c(0,0,0,1,1,1,rep(0,6)),
+ c(rep(0,6),1,1,1,0,0,0),
+ c(rep(0,9),1,1,1))
> colnames(mat) <- c("nu","nt","tu","tt")

Solid tumors

Common three subtypes of solid tumors:
Inv, Pro, Meta
BEZ235, Nilotinib, 5-FU

Mapping illumina to affymetrix

Mapping illumina to affymetrix

http://www.switchtoi.com/probemapping.ilmn