Using limma to analyze GEO datasets/series from two-channel experiments
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@gordon-smyth
Last seen 5 hours ago
WEHI, Melbourne, Australia
Dear Ana, Your code should work already. Analysing log-ratios is the normal way to handle two-colour arrays. Please see the User's Guide which has plenty of examples. Best wishes Gordon > Date: Fri, 2 Oct 2009 15:00:08 -0700 > From: Ana Rodrigues <arodrigues at="" salk.edu=""> > Subject: [BioC] Using limma to analyze GEO datasets/series from > two-channel experiments > To: bioconductor at stat.math.ethz.ch > Content-Type: text/plain; charset=UTF-8 > > Dear Gurus, > I am attempting to analyze a bunch of microarray experiments from the > GEO database. > > I have experience with Affymetrix chips, so it was reasonably simple > to download the datasets/series of interest, retrieve the relevant > columns from the GSM files (figure out whether they were normalized, > logged, etc), and perform the comparisons I need using limma. > > Now I am struggling to do the same for other platforms, in particular, > two-color platforms. > The first few such experiments I have looked at look reasonably > simple. However, I aven't been able to figure out how to obtain a > data structure that lmFit can use from the GSM files. > > I decided to try the GEOquery package to interface with GEO. > > gse <- getGEO("GSE2998") > exprs <- exprs(gse[[1]]) > > The exprs matrix now contains the VALUE column from each GSM file, > which in this particular case is "The log2-transformed ratio of the > Lowess-normalized fluorescence values (Ch2/Ch1) exported from > GeneTraffic". > > For one of the comparisons that I am interested in, there are two > chips of relevance. > GSM65523, with treated Cy3 and untreated Cy5 > GSM65567, with treated Cy3 and untreated Cy5 > > I thought that the best way to compare treated to untreated would be > something like: > targets <- matrix(c("GSM65523", "noHS", "HS", > "GSM65567", "noHS", "HS"), ncol=3, byrow=TRUE, > dimnames=list(NULL, c("SlideNumber", "Cy3", "Cy5"))) > design <- modelMatrix(targets, ref="noHS") > lmFit(exprs, design) > > But, of course, exprs doesn't contain any channel info, just the log > ratio between the channels. > Should I be retrieving different columns from the GSM files? How can I > build a data structure from that data that lmFit can use? Is there a > better way to do simple comparisons of two-channel GEO datasets? > > Thank you so much for any help you can provide! > Best, > Ana
Microarray limma GEOquery Microarray limma GEOquery • 935 views
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