Entering edit mode
Tim
▴
160
@tim-2058
Last seen 10.2 years ago
Hello bioconductor-list subscribers,
I am interested in various approaches to preprocessing and
normalizing
Infinium data, some rather different from Illumina's. I noticed that
the
'beadarray' package has the ability to read in bead-level data, and
while
I'm sure this isn't the most scalable solution, given the way that
Infinium
arrays are structured, the thought occurred that dealing with one
problem at
a time (eg. reading the data into a sensible structure, THEN dealing
with
memory issues perhaps using R.huge etc.) might be a good idea.
From the raw data, I constructed a 'targets' file (attached) and
then
attempted to pull in the bead-level information from a couple of
arrays (so
as not to exceed my laptop's RAM; I have raw data for 72 arrays on 8
slides
to start with):
> Mack <- readIllumina(arrayNames = targets$ArrayName,
targets=targets, backgroundMethod = "none",
singleChannel=FALSE, metrics=TRUE)
Found 2 arrays
Error in order(dat1$ProbeID) : object 'dat1' not found
In addition: Warning message:
In readIllumina(arrayNames = targets$ArrayName, targets = targets, :
No annotation package was specified.
Need to use SetAnnotation later
The data structure 'dat1' is buried within a switch statement and each
branch can apparently throw the error message seen above. I assume
that,
once I get the data read into a reasonable form, I can deal with the
lack of
annotation files later (in fact, I ought to be able to extract that
from
Illumina's own manifest, correct?). But the current error is puzzling
me
and there is no point (for my project) working with anything other
than
bead-level data. On the off chance that someone else has seen this
before,
I figured I'd try the list.
Any assistance, suggestions, constructive criticism ("hey why aren't
you
using 'otherpackage'!?!"), etc. would be most appreciated.
Thanks in advance,
--tim
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