gravatar for MatthewP

2 hours ago by


Hello, everyone. I want to download and analysis dataset GSE149940 with limma, but there are some small questions I want to ask even after I did read some materials.
I can get expression matrix with _GEOquery_.

gse <- getGEO(filename = matrixPath, destdir = sourceDir, getGPL = FALSE, AnnotGPL = FALSE)
expr1 <- exprs(gse)

I've read usersguide of _limma_ package which descripts how to parse 2 color chip data and how to construct design model for this "dye-swap" design data.
I want to know can I parse the expresion matrix expr1 extract with _GEOquery_ to limma to do analysis directly? Or I need to download rawdata from GEO, and parse to _limma_ with read.maimages function? The second way seems quiet complicated to me for I've never accessed any rawdata of microarray before.

By the way, the data processing descripted in GEO is:

Agilent Feature Extraction Software (v was used for background subtraction and LOWESS normalization.
Normalized log10 ratio (Cy3/Cy5) representing test/reference for samples 2301 R – 2354 S, 2351 R – 2309 S, 2317 R – 2314 S, 2343 R – 2284 S, 2343 R – 2284 S, 2358 R – 2355 S, and 2367 R – 2369 S; normalized log10 ratio (Cy5/Cy3) representing test/reference for samples 2354 S – 2301 R, 2309 S – 2351 R, 2314 S – 2317 R, 2284 S – 2343 R, 2355 S – 2358 R, and 2369 S – 2367 R

So this seems how expr1 were produced.

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