Hi Danny,
Depends on what you think is 'easy'. ;-D
Note that the celfiles are read in row by row. This includes all the
poly-A 'landing lights' that the scanner uses to figure out how to
align
the camera. Also note that there is a function in affy called
read.probematrix(), which just reads the data from multiple celfiles
into a matrix, where the row of the matrix corresponds to the 'index'
location of the probe on the array.
The mapping file you reference has this sort of data:
AT1G01010_at 1 + 3783 1193 1062 NA
AT1G01010_at 1 + 3888 980 824 NA
AT1G01010_at 1 + 4015 927 176 NA
AT1G01010_at 1 + 4195 1542 695 NA
AT1G01010_at 1 + 4525 1527 762 NA
AT1G01010_at 1 + 4712 760 830 NA
AT1G01010_at 1 + 4789 1239 6 NA
AT1G01010_at 1 + 4860 626 38 NA
AT1G01010_at 1 + 5009 1021 7 NA
Where the columns are (in order)
Probe ID
Chr
Strand
Start
X
Y
Probeset name (which is NA, as there are no probesets)
So you have the (x,y) coordinates of the probes on the chip, and where
the probes are in the genome, but when you read the data in you just
have the index position. So you need to convert the (x,y) coordinates
to
the index positions.
There is a function in affy called xy2indices that you can use to
convert things. All you need to know is the number of columns in the
array, which you can get from read.celfile.header().
So you could hypothetically read in the data using read.probematrix(),
normalize using (probably easiest) normalizeBetweenArrays() from
limma,
convert the (x,y) probe locations to indices, merge things
appropriately, and then if you want to be really cool, put all that
into
a GRanges object so you can use things like Gviz to make sweet plots.
Best,
Jim
On 6/3/2014 11:07 AM, Danny Arends wrote:
> Hey James,
>
> Thanks for your answer, I'll look into your suggestions...
>
> However just to be sure, is there an 'easy' hack to get the probes
out
> of the CDF file and match them to the CEL file information?
>
> I have available found the following files that describe the array:
> cdf.gz
> desc.txt.gz
> mapping.txt.gz
> probe_tab.txt.gz
>
> Just getting the probe locations or sequences is enough, then I
could
> start the analysis myself
> (either by mapping probes to the reference using blast, or using the
> supplied locations),
>
> I was hoping that I could use the Affy package for normalization of
> probe intensities, etc
>
> Gr,
> Danny
>
>
>
> 2014-06-02 21:49 GMT+02:00 James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">>:
>
> Hi Danny,
>
>
> In general, you don't use the makecdfenv/affy pipeline for
tiling
> arrays, as there aren't (to my knowledge) any probesets.
Instead,
> there are just probes, tiled along the genome.
>
> The affy package is predicated upon the idea that a set of
probes
> are all grouped into a probeset, which is intended to measure
the
> expression of a transcript. Since the tiling arrays are
completely
> different, the two don't really mix.
>
> Normally I would point you to the oligo package, but you need to
> build a pdInfoPackage, which expects a bpmap file, not a cdf. In
> addition, I tried to read in the cdf that you can get from GEO
using
> readCdfUnits() from affxparser, and it consistently segfaulted,
so
> there might be a problem with the cdf itself.
>
> Looking around, it appears you might be better served by using
> either aroma (
http://www.aroma-project.org/__), which is
supposed to
> handle tiling arrays (but since aroma uses affxparser, maybe it
> won't work).
>
> Or you could try Affy's software:
>
>
http://www.affymetrix.com/__estore/partners_programs/__programs/
developer/__TilingArrayTools/index.affx
> <http: www.affymetrix.com="" estore="" partners_programs="" programs="" dev="" eloper="" tilingarraytools="" index.affx="">
>
> Best,
>
> Jim
>
>
>
>
> On 6/2/2014 2:55 PM, Danny Arends wrote:
>
> Hey,
>
> I got a bug trying to create a custom cdf environment, which
I
> need to
> analyse some affy arrays:
>
> Both functions give the same error:
>
> >
>
make.cdf.package("GPL16303___TilingatSNPtilx520433_At___TAIRG.cdf",
> species="Arabidopsis_Thaliana"__)
> Reading CDF file.
> Creating CDF environment
> Wait for about 0 dots
> Error in assign(x[i], value[[i2]], envir = envir, inherits =
> inherits) :
> invalid first argument
>
> > env <-
>
make.cdf.env("GPL16303___TilingatSNPtilx520433_At___TAIRG.cdf")
> Reading CDF file.
> Creating CDF environment
> Wait for about 0 dots
> Error in assign(x[i], value[[i2]], envir = envir, inherits =
> inherits) :
> invalid first argument
>
> My R version:
> > version
> platform x86_64-pc-linux-gnu
> arch x86_64
> os linux-gnu
> system x86_64, linux-gnu
> status
> major 3
> minor 1.0
> year 2014
> month 04
> day 10
> svn rev 65387
> language R
> version.string R version 3.1.0 (2014-04-10)
> nickname Spring Dance
>
> Is there any fix for this???, because I really wanna look
into
> my array
> data...
>
> Gr,
> Danny Arends
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
