How to convert a "xxx.CEL" file to a "yyy.txt" file?
Viking
to do it.
Can somebody please help me? Thanks a lot.
Viking
Henrik Bengtsson
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
>
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Liang Cheng
Henrik Bengtsson
> Thank you, Henrik
>
> So there is no function from aroma package, which can deal with the "xx.cel"
> file?
Please explain what you mean "deal with". There are hundreds of
methods in the aroma.affymetrix package that process CEL files in
various ways.
/Henrik
Liang Cheng
Henrik Bengtsson
> I want to read the data in it and then process it.
> so: the method to read it & all kinds of methods to process it
I am sorry, but that is still an extremely vague specification of what
you are going to do.
The best I can tell you is to have a look at the various vignettes
online - http://www.aroma-project.org/ - to get a feel on the vast
number of alternatives you have. You probably also want to look at
the various Bioconductor packages supporting Affymetrix data -
http://www.bioconductor.org/.
/Henrik