[aroma.affymetrix] Re: about pgf/clf files

2009-06-08 Thread Henrik Bengtsson
On Mon, Jun 8, 2009 at 8:18 PM, chunjiang he wrote: > Hi, > > Thanks. > I also have some questions when I use the apt-cel-transformer tool. > Does the command like this: > > apt-cel-transformer.exe --clf-file MoEx-1_0-st-v1.r2.clf -c rma.bg... -o > output *.cel > > I cannot run through it on my co

[aroma.affymetrix] Re: about pgf/clf files

2009-06-08 Thread chunjiang he
Hi, Thanks. I also have some questions when I use the apt-cel-transformer tool. Does the command like this: apt-cel-transformer.exe --clf-file MoEx-1_0-st-v1.r2.clf -c rma.bg... -o output *.cel I cannot run through it on my computer. And how I can run a batch of cel files in a folder. Thanks a l

[aroma.affymetrix] Re: SNP6 CNV analysis with Technical replicates

2009-06-08 Thread Henrik Bengtsson
Hi. On Mon, Jun 8, 2009 at 1:53 PM, marco wrote: > > Dear Henrik, > >  I have 2 samples hzbridiyed on SNP6 in respctively 5 and 6 > replicates. I would like to pool them ann estimate the relative CNVs. > Is this fragment of code doing that? Or you have any other > suggestions? > > > cdf      <- A

[aroma.affymetrix] SNP6 CNV analysis with Technical replicates

2009-06-08 Thread marco
Dear Henrik, I have 2 samples hzbridiyed on SNP6 in respctively 5 and 6 replicates. I would like to pool them ann estimate the relative CNVs. Is this fragment of code doing that? Or you have any other suggestions? cdf <- AffymetrixCdfFile$fromChipType("GenomeWideSNP_6", tags="Full") print

[aroma.affymetrix] Re: about pgf/clf files

2009-06-08 Thread Lakshmanan Iyer
Hi It should be available as part of the Affy libraries. check out: http://www.affymetrix.com/support/technical/libraryfilesmain.affx -Lax On Mon, Jun 8, 2009 at 10:40 AM, chunjiang he wrote: > Hi all, > > Anyone can help me? I am looking for: > pgf/clf files for exon array analysis (mouse and h

[aroma.affymetrix] about pgf/clf files

2009-06-08 Thread chunjiang he
Hi all, Anyone can help me? I am looking for: pgf/clf files for exon array analysis (mouse and human) CustomCDF mappings tools for summarizing. Thanks a lot. Best, Jiang --~--~-~--~~~---~--~~ When reporting problems on aroma.affymetrix, make sure 1) to run the la