converting affybatch object to matrix
Use exprs on the output from RMA (or another method you like)
library("affy")
myData <-ReadAffy()
myRMA <- rma(myData)
e = exprs(myRMA)
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Bioconductor-related topics are discussed.
On Fri, Apr 1, 2011 at 9:54 AM, Landes, Ezekiel
<Ezekiel_Landes at hms.harvard.edu> wrote:
I have an Affybatch object called "batch" :
batch
AffyBatch object size of arrays=1050x1050 features (196 kb) cdf=HuGene-1_0-st-v1 (32321 affyids) number of samples=384 number of genes=32321 annotation=hugene10stv1 notes=
Is there a way of converting a portion of this data into a matrix? More specifically, a matrix where the 384 samples are columns and the 32321 genes are rows? The "exprs" function returns a matrix that has 384 columns but for some reason there are 1050^2 rows. Thanks!
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