Hi Viking,
On Tue, Jun 22, 2010 at 6:28 PM, Viking <vikingch...@gmail.com> wrote:
> I am new to aroma-project. I didn't find some materials to learn how
> to do it.
>
> Can somebody please help me? Thanks a lot.
although you new here, please allow me to use a bit of sarcasm,
because then I can award you the price of 'Posting The Least Precise
Question' on the list during the last four years ;)
More seriously, what are you trying to do? A CEL file contains (avg.
intensity, std.dev. of intensity, nbr of pixels) for each probe. In
addition to this there is some information about probes flagged as
outliers by the Affymetrix scanner/image analysis software. You can
find more information in the help pages of the affxparser software.
There is not information about probesets, genes etc. Just so you
know.
The easiest to access all the information in a CEL file is probably
use the low-level affxparser package and its readCel() function, e.g.
pathname <- "0001-7,10K,15-08-2006.CEL";
data <- readCel(pathname, readXY=TRUE, readIntensities=TRUE,
readStdvs=TRUE, readPixels=TRUE);
List of 8
$ header :List of 14
..$ filename : chr "C:/Users/hb/Documents/My Data/rawData/Jeremy_2007-10k
/Mapping10K_Xba142/0001-7,10K,15-08-2006.CEL"
..$ version : int 4
..$ cols : int 658
..$ rows : int 658
..$ total : int 432964
..$ algorithm : chr "Percentile"
..$ parameters : chr "Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierL
ow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:5;FullFeatureH"| __t
runcated__
..$ chiptype : chr "Mapping10K_Xba142"
..$ header : chr "Cols=658\nRows=658\nTotalX=658\nTotalY=658\nOffsetX=0
\nOffsetY=0\nGridCornerUL=235 130\nGridCornerUR=3603 136\nGridCornerLR=359"| __t
runcated__
..$ datheader : chr "[25..29720] 0001-7 10K 15-08-2006:CLS=3715 RWS=3715
XIN=1 YIN=1 VE=30 2.0 08/15/06 10:02:13 50206820 M10 \024 \02"| __t
runcated__
..$ librarypackage: chr ""
..$ cellmargin : int 2
..$ noutliers : int 1527
..$ nmasked : int 0
$ x : int [1:432964] 0 1 2 3 4 5 6 7 8 9 ...
$ y : int [1:432964] 0 0 0 0 0 0 0 0 0 0 ...
$ intensities: num [1:432964] 271 16038 282 17471 138 ...
$ stdvs : num [1:432964] 34.9 2321.7 36 3107.4 16.9 ...
$ pixels : int [1:432964] 9 9 9 9 9 9 9 9 9 9 ...
$ outliers : int [1:1527] 272 307 345 360 486 624 952 1019 1037 1155 ...
$ masked : NULL
See help("readCel", package="affxparser") for more information.
Then you can write whichever fields you like to to file.
Hope this helps
Henrik
>
> Viking
>
> --
> 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.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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