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
>
> --
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>
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--
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version of the package, 2) to report the output of sessionInfo() and
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