Thank you, Henrik
So there is no function from aroma package, which can deal with the "xx.cel"
file?
Viking
2010/6/22 Henrik Bengtsson <h...@stat.berkeley.edu>
> 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.
> >
> >
> > You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
> >
>
> --
> 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/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>
--
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/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
