Question: Nimblegen Arrays and Ringo
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gravatar for Dario Strbenac
9.0 years ago by
Dario Strbenac1.5k
Australia
Dario Strbenac1.5k wrote:
Hello, I've been looking at the NDF of a certain chip (2007-09-21_MM8_Deluxe_Promoter_HX1.ndf) and the pair files. I've noticed that in the NDF there are 5 types of probes - "BLOCK1" "H_CODE" "NGS_CONTROLS" "RANDOM" "V_CODE". But in the pair files, there is just "BLOCK1" and "RANDOM". Why are the other 3 types not in the results ? Also does anyone know what the categories actually mean ? There isn't any explanation in the official document that comes with the arrays from the manufacturer (NimbleGen_Data_Formats_v2p1.pdf) or online. -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia
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ADD COMMENTlink modified 9.0 years ago by Laurent Gautier2.2k • written 9.0 years ago by Dario Strbenac1.5k
Answer: Nimblegen Arrays and Ringo
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gravatar for Laurent Gautier
9.0 years ago by
Laurent Gautier2.2k
Laurent Gautier2.2k wrote:
The NimbleGen image analysis software can output the results to different formats (pairs, xys, ...), all containing slightly different information for a given hybridization. The NDF is the most complete description for the probes on a given array, and there is no need to repeat that information in all pairs/xys/whatever files. Regarding the meaning of the categories, the types can vary from array to array. NGS_CONTROLS can be internal controls for placing the grid during image analysis. You can mostly make sense of them by looking at the corresponding text in the other columns (DESIGN_NOTE for example). ** Otherwise, this is not directly related to bioconductor and may be the NimbleGen technical support would answer this better ? L. On 01/12/10 06:00, Dario Strbenac wrote: > Hello, > > I've been looking at the NDF of a certain chip (2007-09-21_MM8_Deluxe_Promoter_HX1.ndf) and the pair files. I've noticed that in the NDF there are 5 types of probes - "BLOCK1" "H_CODE" "NGS_CONTROLS" "RANDOM" "V_CODE". But in the pair files, there is just "BLOCK1" and "RANDOM". Why are the other 3 types not in the results ? Also does anyone know what the categories actually mean ? There isn't any explanation in the official document that comes with the arrays from the manufacturer (NimbleGen_Data_Formats_v2p1.pdf) or online. > > -------------------------------------- > Dario Strbenac > Research Assistant > Cancer Epigenetics > Garvan Institute of Medical Research > Darlinghurst NSW 2010 > Australia > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 9.0 years ago by Laurent Gautier2.2k
The H_CODE, V_CODE, and NGS_CONTROLS containers contain features only associated with synthesis QC and alignment, and so are not exported in a .pair file unless the "Include controls?" box is checked in the Pair Report dialog in NimbleScan. Since those features are of little or no utility for analysis after an experimental hybridization, they are not included in pair reports by default. Those three containers will be contained on all array designs. The remaining containers (from 1 to N) can be named a variety of different names. BLOCK1 through BLOCKN are typical names for containers containing replicate probes (or sometimes FORWARD/REVERSE), and the RANDOM container contains randomly generated probes with the same length and GC composition as the experimental probes which can be used to estimate non-specific binding. Container naming is often up to the customer and so they can vary a great deal. Todd On Wed, Dec 1, 2010 at 12:32 AM, Laurent Gautier <laurent@cbs.dtu.dk> wrote: > > The NimbleGen image analysis software can output the results to > different formats (pairs, xys, ...), all containing slightly different > information for a given hybridization. The NDF is the most complete > description for the probes on a given array, and there is no need to > repeat that information in all pairs/xys/whatever files. > > Regarding the meaning of the categories, the types can vary from array > to array. NGS_CONTROLS can be internal controls for placing the grid > during image analysis. You can mostly make sense of them by looking at > the corresponding text in the other columns (DESIGN_NOTE for example). > ** > Otherwise, this is not directly related to bioconductor and may be the > NimbleGen technical support would answer this better ? > > > L. > > On 01/12/10 06:00, Dario Strbenac wrote: > > Hello, > > > > I've been looking at the NDF of a certain chip > (2007-09-21_MM8_Deluxe_Promoter_HX1.ndf) and the pair files. I've noticed > that in the NDF there are 5 types of probes - "BLOCK1" "H_CODE" > "NGS_CONTROLS" "RANDOM" "V_CODE". But in the pair files, there is just > "BLOCK1" and "RANDOM". Why are the other 3 types not in the results ? Also > does anyone know what the categories actually mean ? There isn't any > explanation in the official document that comes with the arrays from the > manufacturer (NimbleGen_Data_Formats_v2p1.pdf) or online. > > > > -------------------------------------- > > Dario Strbenac > > Research Assistant > > Cancer Epigenetics > > Garvan Institute of Medical Research > > Darlinghurst NSW 2010 > > Australia > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Todd Richmond richmond.todd@gmail.com [[alternative HTML version deleted]]
ADD REPLYlink written 9.0 years ago by Todd Richmond30
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