[aroma.affymetrix] Re: script difference in out put in snp 6.0
No worries at all - I just want you and everyone else to know how to make this forum more effective, which is somewhat explained in that FAQ. 2008-03-26: http://groups.google.com/group/aroma-affymetrix/web/frequently-asked-questions Cheers, Henrik On Tue, Sep 1, 2009 at 11:58 AM, ssvssv@gmail.com wrote: 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 'reply' button (which is a mistake again). I appreciate that you spend your valuable time to answer many questions over here. Thanks once again for the answer. --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: script difference in out put in snp 6.0
On Mon, Aug 31, 2009 at 11:42 PM, ssvssv@gmail.com wrote: Hi Henrik Here are the links: 1) http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0 Under Identification of copy-number regions cbs - CbsModel(ces1, ces2) From the vignette and section your referring to: In order to do paired analysis using the Circular Binary Segmentation (CBS) method, do: cbs - CbsModel(ces1, ces2) where 'ces1' is a CEL set of test samples and 'ces2' is a CEL set of the same number of control samples. Use ces1 - extract(cesN, arrays1) and same for 'ces2' to extract the two sets from the 'cesN' CEL set above. Whenever you specify two *sets*, you tell the segmentation model that you want to do a paired/matched analysis. If so, the model calculate ratios between the first array in ces1 and the first in ces2, between the seconf in ces1 and the second in ces2, and so on. Therefore, if 'ces1' and 'ces2' are *sets*, they must contain the same number of arrays (otherwise an error will be thrown). 2) In windows, under C:\Program Files\R\R-2.9.1\library \aroma.affymetrix\testScripts\system\chipTypes\GenomeWideSNP_6, R script file by name test20080729,6.0,CN,refSet.R FYI, those are not really user example scripts, but the redundancy/system tests that we run at each release to make sure everything works as expected and that new updates doesn't break old functions. Of course, you may still look at them, because most imitate real scenarios. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Segmentation with specific reference set # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Use the robust average of the first three arrays as a reference cesR - extract(cesN, 1:3); ceR - getAverageFile(cesR); print(ceR); sm - CbsModel(cesN, ceR); As print(cesN), print(cesR), and print(ceR) confirms, 'cesN' is a data *set* with 6 arrays (the s in ces indicates set), 'cesR' is a subset of 'cesN' with 3 arrays, and 'ceR' is a single array/file (no s). 'ceR' is a single array in the sense that it is a robust average of the 3 arrays. Next, you set up a segmentation model where you want to segment the 6 arrays in the *set* using one *array* as a reference. This is interpreted as you want to use the same reference for each of the 6 arrays. = So in my context, i translated that as given below: Analysis is done on two paired samples (normal1: tumor1). Script 1 (Link 1) = # Use the robust average of the first array as a reference cesR - extract(cesN, 1); cesL - extract(cesN, 2); sm-CbsModel(cesR,cesL) Note, extract() extracts a *set* of arrays, so you are asking for a paired analysis. The CN ratios are hence calculated between the first array in 'cesR' and the first array in 'cesL' (that's all arrays there is). (FYI, for extracting single arrays there is getFile()). = Script 2 (from the link 2: modified example script) # Use the robust average of the first array as a reference cesR - extract(cesN, 1); cesL - extract(cesN, 2); ceR - getAverageFile(cesR); sm - CbsModel(cesN, ceR); 'cesN' is a set (of six arrays from the example) and 'ceR' is an (robust average) *file*, so no paired analysis but a common reference. = First question would be: did I cross stitch two different methods (analyses) and came up with a hybrid script :(? Yes. It is easier to help you if you instead say what you want to do. ...and using print(cesR) etc to see what is going on. Cheers, Henrik If not, second one would be , what is the difference ? Regards 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 received this message because you are subscribed to the Google Groups aroma.affymetrix group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
[aroma.affymetrix] Re: script difference in out put in snp 6.0
On Tue, Sep 1, 2009 at 7:53 AM, Henrik Bengtssonhenrik.bengts...@gmail.com wrote: On Mon, Aug 31, 2009 at 11:42 PM, ssvssv@gmail.com wrote: Hi Henrik Here are the links: 1) http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0 Under Identification of copy-number regions cbs - CbsModel(ces1, ces2) From the vignette and section your referring to: In order to do paired analysis using the Circular Binary Segmentation (CBS) method, do: cbs - CbsModel(ces1, ces2) where 'ces1' is a CEL set of test samples and 'ces2' is a CEL set of the same number of control samples. Use ces1 - extract(cesN, arrays1) and same for 'ces2' to extract the two sets from the 'cesN' CEL set above. Whenever you specify two *sets*, you tell the segmentation model that you want to do a paired/matched analysis. If so, the model calculate ratios between the first array in ces1 and the first in ces2, between the seconf in ces1 and the second in ces2, and so on. Therefore, if 'ces1' and 'ces2' are *sets*, they must contain the same number of arrays (otherwise an error will be thrown). 2) In windows, under C:\Program Files\R\R-2.9.1\library \aroma.affymetrix\testScripts\system\chipTypes\GenomeWideSNP_6, R script file by name test20080729,6.0,CN,refSet.R FYI, those are not really user example scripts, but the redundancy/system tests that we run at each release to make sure everything works as expected and that new updates doesn't break old functions. Of course, you may still look at them, because most imitate real scenarios. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Segmentation with specific reference set # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Use the robust average of the first three arrays as a reference cesR - extract(cesN, 1:3); ceR - getAverageFile(cesR); print(ceR); sm - CbsModel(cesN, ceR); As print(cesN), print(cesR), and print(ceR) confirms, 'cesN' is a data *set* with 6 arrays (the s in ces indicates set), 'cesR' is a subset of 'cesN' with 3 arrays, and 'ceR' is a single array/file (no s). 'ceR' is a single array in the sense that it is a robust average of the 3 arrays. Next, you set up a segmentation model where you want to segment the 6 arrays in the *set* using one *array* as a reference. This is interpreted as you want to use the same reference for each of the 6 arrays. = So in my context, i translated that as given below: Analysis is done on two paired samples (normal1: tumor1). Script 1 (Link 1) = # Use the robust average of the first array as a reference cesR - extract(cesN, 1); cesL - extract(cesN, 2); sm-CbsModel(cesR,cesL) Note, extract() extracts a *set* of arrays, so you are asking for a paired analysis. The CN ratios are hence calculated between the first array in 'cesR' and the first array in 'cesL' (that's all arrays there is). (FYI, for extracting single arrays there is getFile()). = Script 2 (from the link 2: modified example script) # Use the robust average of the first array as a reference cesR - extract(cesN, 1); cesL - extract(cesN, 2); ceR - getAverageFile(cesR); sm - CbsModel(cesN, ceR); 'cesN' is a set (of six arrays from the example) and 'ceR' is an (robust average) *file*, so no paired analysis but a common reference. = First question would be: did I cross stitch two different methods (analyses) and came up with a hybrid script :(? Yes. It is easier to help you if you instead say what you want to do. ...and using print(cesR) etc to see what is going on. ...from a private followup email message(*): This almost solved my problem in analysis except for that last part. Scenario is like this: I have one control sample for multiple tumors and I wanted them to be compared pairwise. For eg. Normal sample N1, Tumor samples T1, T2, T3, T4 and I need them to be compared like this : N1, T1; N1,T2; N1,T3. So, assume that you processed everything together in a set 'cesN' of, say, 12 arrays, and that the tumors have index 3,4, 9 and 11, and the normal has index 2. The you want to do: # The set containing the 4 tumor samples cesTumor - extract(cesN, c(3,4,9,11)); # The single normal sample (as a reference for all) ceNormal - getFile(cesN, 2); cbs - CbsModel(cesTumor, ceNormal); This will process the 4 arrays in 'cesTumor'. The remaining in 'cesN' will not be processed. Hope this helps (*) Please don't send private messages - 'FAQ. 2008-03-26: Why do you not want to answer questions sent to your private email address?': http://groups.google.com/group/aroma-affymetrix/web/frequently-asked-questions Henrik Cheers, Henrik If not, second one would be , what is the difference ? Regards suresh --~--~-~--~~~---~--~~ When reporting problems on
[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 'reply' button (which is a mistake again). I appreciate that you spend your valuable time to answer many questions over here. Thanks once again for the answer. --~--~-~--~~~---~--~~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~--~~~~--~~--~--~---
