Hi everyone,
I am starting to analyse some tiling arrays, but I
cannot find the corresponding CDF file in bioconductor (for example
hs35bm03rv02cdf or hs35bm03rv02cdf).
What I am exactly looking for is to know the position (or index) of
the
perfect matches and the corresponding sequence. Is there any way to do
it?
Thank you in advance,
Alessandro
______________________________________________________________________
______________
Finding fabulous fares is fun.
The tiling arrays do not have a CDF, they use a BPMAP instead, which
can be used in conjunction with the makePlatformDesign package to
create a data package, which is in turn used by the oligo package to
read in the CEL files.
How many samples are you going to be working with? This will require
you a good amount of memory....
b
On Apr 3, 2007, at 10:07 AM, Alessandro Ferrantini wrote:
> Hi everyone,
> I am starting to analyse some tiling arrays, but I
> cannot find the corresponding CDF file in bioconductor (for example
> hs35bm03rv02cdf or hs35bm03rv02cdf).
> What I am exactly looking for is to know the position (or index) of
> the
> perfect matches and the corresponding sequence. Is there any way to
do
> it?
>
> Thank you in advance,
>
> Alessandro
>
>
>
>
>
______________________________________________________________________
> ______________
> Finding fabulous fares is fun.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/
> gmane.science.biology.informatics.conductor
Dear Benilton,
Thanks a lot for your suggestion. I've installed R version 2.5 and
makePlatformDesign and oligo packages. I've tried the following:
> makePDpackage("Hs35b_M01R_v01_NCBIv35.bpmap",type="tiling",genomebui
ld="hg15")
but I got an error:
affymetrix tiling
Error in makePDpackage("Hs35b_M01R_v01_NCBIv35.bpmap", type =
"tiling", :
could not find function "cleanPlatformName"
Any ideas? Here below the sessionInfo.
Thank you,
Alessandro
> sessionInfo()
R version 2.5.0 alpha (2007-04-01 r41004)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.
UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8
;LC_IDENTIFICATION=C
attached base packages:
[1] "splines" "tools" "stats" "graphics" "grDevices"
"utils"
[7] "datasets" "methods" "base"
other attached packages:
makePlatformDesign oligo BufferedMatrixMethods
"0.99.24" "0.99.96" "0.1.1"
BufferedMatrix RSQLite DBI
"0.1.29" "0.5-3" "0.2-1"
Biobase affyio
"1.13.47" "1.3.3"
______________________________________________________________________
______________
The fish are biting.
