Hi,
Have you tried using extractAffyBatch, which is documented here:
http://aroma-project.org/howtos/extractAffyBatch ?
As far as I understand you will need the Bioconductor annotation
package corresponding to your chip type to be installed, ie
source(http://www.bioconductor.org/biocLite.R;)
Perhaps something like this is what you want (note: different chip to
what you are using)?
df - readDataFrame(getCdf(cs), verbose=-80)
[...snip...]
head(df)
unit unitName unitType unitDirection unitNbrOfAtoms group groupName
11 7892501 expression sense 4 1
Hi Mark:
My idea is how we could know the intensity for each probe ? Using
these command:
library(aroma.affymetrix)
cs - AffymetrixCelSet$byName(KN01M013, chipType=HG-U133_Plus_2)
raw=extractMatrix(cs,verbose=verbose)
I can see 'raw' is a list of intensities, but I don't know which probe
ids
How about grabbing the intensities according to their index:
raw=extractMatrix(cs,cells=df$cell,verbose=verbose)
Then you'll have them matched up to the 'df' data.frame.
(Different numbers for your chip, of course)
dim(df)
[1] 844550 16
dim(raw)
[1] 844550 33
Mark
On Aug 10, 2011,
