[aroma.affymetrix] Re: extracting unit IDs and corresponding SNPs

I figured it out. Thanks suresh --~--~-~--~~~---~--~~ 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

[aroma.affymetrix] extracting unit IDs and corresponding SNPs

Hi rawCNs - extractRawCopyNumbers(cbs, array=1, chromosome=1) After this step from the tutorial, http://groups.google.com/group/ aroma-affymetrix/web/total-copy-number-analysis-6-0, I want to write SNPs and their corresponding rawCNs to a file. rawCNs gives units and corresponding CN

[aroma.affymetrix] multiple cel file location

Hi During analysis, i observed that cel files are copied to multiple directories. Original (starting) place to keep all files is in rawData. But all folders in probe data have same copies of cel files which occupies a large chunk of hard disk space. In my case, I have pcancer,ACC,ra,-XY,

[aroma.affymetrix] Re: script difference in out put in snp 6.0

Hi Henrik That was an inadvertent mistake and I am sorry. I was looking at another older post ( by title: use a few normal samples as the reference set ). My doubts were almost cleared with that post and I had a small doubt. I could not find reply button and i thought reply to author button is

[aroma.affymetrix] Re: copy number calls in the output

Hi Pierre Thanks for the answer. we were comparing one of the HMM models with CBS and GLAD. I will try haarseg too. some times (my) ignorance is embarrassing. suresh --~--~-~--~~~---~--~~ When reporting problems on aroma.affymetrix, make sure 1) to run the

[aroma.affymetrix] benchmarking CN analysis with aroma.affymetrix (with CBS)

Hi Henrik I was benchmarking aroma.affymetrix performance on 72 affymetrix 250k sty files (36 normal, 36 tumor- paired analysis). Here is what I have so far: == 1) setting up CEL sets and locating the CDF file usersystem elapsed 7.441.28

[aroma.affymetrix] copy number calls in the output

Hi Henrik Here is another question. I was trying to compare ouput from cbs model with that from glad model. After processing, (.tsv) xls files are created in respective directories. While xls (.tsv) file for glad model has copy number calls written to the file (neutral, gain and loss), cbs file

Re: CbsModel same as CBS in DNAcopy? (Was: Re: [aroma.affymetrix] Re: cbs_error_in_250k_sty_cn_analysis_)

Thanks henrik :) --~--~-~--~~~---~--~~ 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

[aroma.affymetrix] Re: cbs_error_in_250k_sty_cn_analysis_

Hi Henrik Thanks for the reply. I was able to troubleshoot the problem. I was analyzing sty chips and in chip types, I included both the chips (sty and nsp). Since there are no corresponding cel files (nsp), it was generating lists with null values. Once i sorted that out, every thing worked

[aroma.affymetrix] cbs_error_in_250k_sty_cn_analysis_

Hi All I am analyzing 250k sty samples (only) (paired: healthy Vs tumor). No. of samples around 72 (36 each, paired). I am following the tutorial posted on http://groups.google.com/group/aroma-affymetrix/web/paired-total-copy-number-analysis. Till identification of copy-number regions in