Hi.
Yes, to extract all cell (=probe) intensities from all arrays in an
AffymetrixCelSet ('csN'), you can do:
Y <- extractMatrix(csN, drop=FALSE)
Typically an Affymetrix array contains several million probes, so this
will be a rather big matrix, especially if you have many arrays.
More comments below...
On Mon, Jun 11, 2012 at 1:50 PM, sean nj <[email protected]> wrote:
> Hi guys,
>
> I have a weird situation that I need to retrieve probe level intensity (not
> the probeset/gene level) from U133Plus2 expression array data. I did RBC and
> qn first.
>
>> library(aroma.affymetrix)
>> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
>> chipType <- "HG-U133_Plus_2,Binary,Hs_ENTREZG"
>> cdf <- AffymetrixCdfFile$byChipType(chipType)
>> cs <- AffymetrixCelSet$byName("Genesis_Lung", cdf=cdf)
>> bc <- RmaBackgroundCorrection(cs)
>> csBC <- process(bc,verbose=verbose)
>> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
>> csN <- process(qn, verbose=verbose)
>> print(csN)
> .....
>
> At first, I tried to save the data into a table, but had no success.
>
>> data <- readUnits(csN)
This returns a special list/tree that reflects the structure of the
CDF associated with the 'csN' object.
>> write.table(data,"myfile.txt",sep="\t")
Here you're trying to use write.table() to write that tree structure
to file; it does not work/does not make sense, because write.table()
writes tabular text files.
> Error in data.frame(`AFFX-BioB-5_at` = list(`AFFX-BioB-5_at` =
> list(intensities = c(6.21948575973511, :
> arguments imply differing number of rows: 40, 22, 138, 16, 38, 108, 28,
> 42, 36, 44, 18, 64, 20, 60, 14, 32, 34, 24, 10, 8, 12, 48, 6, 46, 128, 106,
> 54, 26, 52, 88, 56, 62, 82, 66, 70, 74, 76, 58, 86, 30, 78, 80, 96, 102, 84,
> 142, 50, 100, 116, 110, 68, 146, 120, 90, 98, 92, 148, 134, 122, 118, 72,
> 144, 126, 104, 150, 124, 162, 136, 130, 114, 94, 112, 132, 216, 154, 140,
> 168, 172, 152, 160, 170, 182, 178, 166, 180, 198
>>
>
> Then, I tried some method metioned in thread regarding exon array
> (http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/40e3950e52d73c1f)
>
>> cell <- 9049 # 9049 is the unit number corresponding to the probeset
>> 3799_at in custom CDF
>> Y <- extractMatrix(csN, cells=cells, field=c("intensities", "stdvs",
>> "pixels"), drop=FALSE, verbose=verbose)
> Error in extractMatrix.AffymetrixCelSet(csN, cells = cells, field =
> c("intensities", :
> object 'cells' not found
Note that you ask extractMatrix() to use the value of object 'cells'
and assign it to the argument named 'cells'. The error is simple; it
says that you do not have an object 'cells'. You do have one named
'cell', though.
Regardless, you're are interesting in the probeset named '3799_at'.
(To be picky, a probe set is formally called *unit group*, because
each CDF *unit* can contain multiple *groups*. However, assuming that
each unit of your CDF only got one group, we can say that the probeset
corresponds to one unit.) This corresponds to index 9049, which I
assume you inferred by:
cdf <- getCdf(csN);
unit <- indexOf(cdf, names="3799_at");
Note that a *unit* is not a *cell*. A *cell* is a single probe. A
unit contains unit groups, which in turn contains cells. So, if
you're interested in the cells (=probes) of a single unit, you need to
do something like:
> cells <- getCellIndices(cdf, unit=4024, unlist=TRUE);
> str(cells)
Named int [1:22] 250694 251858 25400 26564 1273099 1274263 406504 407668 124536
1 1246525 ...
- attr(*, "names")= chr [1:22] "204435_at.groups.204435_at.indices1" "204435_at
.groups.204435_at.indices2" "204435_at.groups.204435_at.indices3" "204435_at.gro
ups.204435_at.indices4" ...
and then
Y <- extractMatrix(csN, cells=cells, drop=FALSE);
For your information, the following illustrates the CDF unit group
cell structure:
> cells <- getCellIndices(cdf, unit=4024);
> str(cells);
List of 1
$ 204435_at:List of 1
..$ groups:List of 1
.. ..$ 204435_at:List of 1
.. .. ..$ indices: int [1:22] 250694 251858 25400 26564 1273099 1274263 406504
407668 1245361 1246525 ...
I recommend you to play around with the 'affxparser' package to learn
more about the CDF structure.
Hope this helps
/Henrik
> At last, I repeated the above without "cells=cells" and it seemed working
> with no error message. But I am not sure if this is the right result or not.
>> Y <- extractMatrix(csN, field=c("intensities", "stdvs", "pixels"),
>> drop=FALSE, verbose=verbose)
>
> Any suggestion?
>
> Thanks a lot for the help!
>
> Sean
>
> --
> 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.
>
>
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--
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.
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