Hi Maria. On Wed, Jul 6, 2011 at 5:59 AM, Maria Rodrigo-Domingo <mrod...@gmail.com> wrote: > Hi all, > > I am using aroma.affymetrix for an analysis on Human Exon Array data > and would need to access the individual probe intensities mapped to > probe_id after background correction and normalization. Is there an > easy way to do this? Below you can see what I have tried so far. > > With the notation on http://www.aroma-project.org/node/37 I am looking > at object csN - data at probe-level after BC and QN > >> affyBatch <- extractAffyBatch(csN) > # I get an error message about package "huex10stv2cdf" not being > available from Bioconductor.
Yes, that approach, which tries to extract a "Bioconductor" AffyBatch object, is basically just a convenient wrapper around ReadAffy() of the affy package, and that is what needs a 'huex10stv2cdf' package. >> probes_matrix <- extractMatrix(csN, cells=NULL, field=c("intensities", >> "stdvs", "pixels"), drop=FALSE, verbose=verbose) # I do not get any >> information about which probe the intensity belongs to It might be that you've missed that *probes* (aka *cells* as we prefer to call them) do *not* have annotations in Affymetrix arrays. It is only *probesets* (aka *unit groups*) that have annotations. Probesets, which are defined by the CDF you choose, specifies which sets of probes should be grouped together. For example, if you know you are interested in probes 1040-1054, you can extra their probe intensities across all arrays in the AffymetrixCelSet ('csN') as you do: > cells <- 1040:1054; > Y <- extractMatrix(csN, cells=cells, field=c("intensities", "stdvs", > "pixels"), drop=FALSE, verbose=verbose); > str(Y) num [1:15, 1:6] 37 32 96 214 706 29 39 218 39 792 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:6] "huex_wta_cerebellum_A" "huex_wta_cerebellum_B" ... Note how there are column names, which corresponds to the array/sample names, but there are no row names simply because probes don't have names. Probes are specified by the (x,y) coordinates on the array and there is a one-to-one mapping (x,y) <-> probe index. You can read more about this in the help of the affxparser package: > help("2. Cell coordinates and cell indices", package="affxparser") >> intensities <- getIntensities(csN) > # no probe or array information Same reason as above. (Also, I recommend to use extractMatrix() instead of getIntensities()). >> unitIntensities <- getUnitIntensities(csN, verbose=verbose) > # I get transcript and probeset information and the individual > intensities of the 4 probes in each probeset, but numbered 1 to 4, so No we're getting closer. The getUnitIntensities() returns a list structure containing probe intensities. The list structure reflects the structure of the CDF, i.e. which cells belongs to which unit groups. Note how the items in the list have names. These are the so called "unit names". Each item in turn consists of a sublist, which corresponds to the units groups. They also have names which are the so called "group names". > I still cannot map them to their target sequence. Q. So, does this mean that you are interested in finding the genomic location of each probe? Is that the kind of annotation you are looking for when you ask for "probe_id"? Note that when they designed the custom CDFs for FIRMA, they did map the 25-mer probes to the genome by their sequences, cf. subpages via http://aroma-project.org/chipTypes/HuEx-1_0-st-v2 Q. Could it be that you are interested in transcript or exon summaries? See how-to page 'Extract probeset summaries (chip effects) as a data frame' [http://www.aroma-project.org/howtos/extractDataFrame] and the example for 'HuEx-1_0-st-v2' - is that what you're looking for? The answer will depend on what you are really after. /Henrik > > I have now run out of ideas so I would really appreciate any > suggestions. Thank you very much in advance for your help. > > Best regards, > Maria Rodrigo > > PhD student in Biostatistics > Department of Haematology, Medical Center Aalborg Hospital Science and > Innovation Center AHSIC Denmark > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/