Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file

2011-08-09 Thread Mark Robinson
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

[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file

2011-08-09 Thread hsingjun cheung
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

[aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file

2011-08-09 Thread Mark Robinson
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 789250

Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file

2011-08-09 Thread Pierre Neuvial
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";)