CLF/PGF parser
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@kasper-daniel-hansen-2979
Last seen 3 months ago
United States
Hi Jim (with a cc to BioC so other interested parties can take note, and a cc to devnet at affy in case there has been any updates). The strange situation right now is that CLF/PGF files cannot be parsed using the Fusion SDK (Affy's official file parsing SDK). There are codes for parsing the files somewhere inside the source code of the EXACT tools (I think - at least somewhere in the source of one of Affy's programs). We are however loathe to take that code and add it to affxparser because sooner or later, the SDK ought to start supporting CLF/PGF files and then the time spent doing that would be more or less wasted. Of course that decision is easier to make when none of us have a use for parsing these files at the moment. I find it somewhat strange that the file format has not been added to the official SDK yet (I just checked version 1.09 again and I could not find it), and I encourage everyone to mention it to their Affymetrix representatives. As soon as that has been done, we will start incorporating it into affxparser, something that should be a fairly simple task. Kasper On Jun 13, 2007, at 7:49 AM, James MacDonald wrote: > Hi Kasper, > > Do you have any plans to add parsers for CLF/PGF files to affxparser? > > Best, > > Jim > > > -- > > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and > should not be used for urgent or sensitive issues.
Microarray Cancer affy affxparser Microarray Cancer affy affxparser • 498 views
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Xinxia Peng ▴ 120
@xinxia-peng-1881
Last seen 7.1 years ago
Hi All, I want to know if there is a difference between any two samples out of 7 in this situation: I am doing single channel analysis of two color arrays using Limma. The dataset has 7 different samples and each sample has different number of biological replicates (2 to 4). I included an coefficient for each biological replicates in the linear model, considering each biological replicate has different number of technical replicates. The 'Technical Replication' section in Limma's user guide shows an example of making contrast matrix for comparisons of interest. How do I construct a contrast matrix to test if their means are same? Or I need do ANOVA analysis of those fitted coefficients? Thanks, Xinxia
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@james-w-macdonald-5106
Last seen 12 hours ago
United States
Hi Kasper, Kasper Daniel Hansen wrote: > Hi Jim (with a cc to BioC so other interested parties can take note, > and a cc to devnet at affy in case there has been any updates). > > The strange situation right now is that CLF/PGF files cannot be parsed > using the Fusion SDK (Affy's official file parsing SDK). There are > codes for parsing the files somewhere inside the source code of the > EXACT tools (I think - at least somewhere in the source of one of > Affy's programs). We are however loathe to take that code and add it to > affxparser because sooner or later, the SDK ought to start supporting > CLF/PGF files and then the time spent doing that would be more or less > wasted. Of course that decision is easier to make when none of us have > a use for parsing these files at the moment. In the file format document for the pgf files: https://www.affymetrix.com/support/developer/fusion/File_Format_PGF_ap tv161.pdf I find this comment: Parsing and Writing The official C++ parser used by affy can be found in APT under sdk/file/TsvFile/PgfFile.h. When possible, parsing and writing of PGF files should be done using this code. I find the same file in the fusion SDK, along with some other files (like DumpPgf.cpp) that look at least like a start. Is this the sort of thing you need, or are you wanting more complete parser? Best, Jim > > I find it somewhat strange that the file format has not been added to > the official SDK yet (I just checked version 1.09 again and I could not > find it), and I encourage everyone to mention it to their Affymetrix > representatives. As soon as that has been done, we will start > incorporating it into affxparser, something that should be a fairly > simple task. > > Kasper > > On Jun 13, 2007, at 7:49 AM, James MacDonald wrote: > >> Hi Kasper, >> >> Do you have any plans to add parsers for CLF/PGF files to affxparser? >> >> Best, >> >> Jim >> >> >> -- >> >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> >> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues. > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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On Jun 14, 2007, at 12:32 PM, James W. MacDonald wrote: > Hi Kasper, > > Kasper Daniel Hansen wrote: >> Hi Jim (with a cc to BioC so other interested parties can take >> note, and a cc to devnet at affy in case there has been any updates). >> The strange situation right now is that CLF/PGF files cannot be >> parsed using the Fusion SDK (Affy's official file parsing SDK). >> There are codes for parsing the files somewhere inside the source >> code of the EXACT tools (I think - at least somewhere in the >> source of one of Affy's programs). We are however loathe to take >> that code and add it to affxparser because sooner or later, the >> SDK ought to start supporting CLF/PGF files and then the time >> spent doing that would be more or less wasted. Of course that >> decision is easier to make when none of us have a use for parsing >> these files at the moment. > > In the file format document for the pgf files: > > https://www.affymetrix.com/support/developer/fusion/ > File_Format_PGF_aptv161.pdf > > I find this comment: > > Parsing and Writing > The official C++ parser used by affy can be found in APT under > sdk/file/TsvFile/PgfFile.h. When possible, parsing and writing of > PGF files should > be done using this code. > > I find the same file in the fusion SDK, along with some other files > (like DumpPgf.cpp) that look at least like a start. Is this the > sort of thing you need, or are you wanting more complete parser? Well, ahm, it looks like you are better at using grep/find than I am. This looks to be it, although a cursory glance at the files seems to indicate a different structure than what we are used to. This might be because of the use of Tsv stuff. Anyway, before I humiliate myself further, I should take a closer look. Thanks, Kasper > Best, > > Jim > > >> I find it somewhat strange that the file format has not been added >> to the official SDK yet (I just checked version 1.09 again and I >> could not find it), and I encourage everyone to mention it to >> their Affymetrix representatives. As soon as that has been done, >> we will start incorporating it into affxparser, something that >> should be a fairly simple task. >> Kasper >> On Jun 13, 2007, at 7:49 AM, James MacDonald wrote: >>> Hi Kasper, >>> >>> Do you have any plans to add parsers for CLF/PGF files to >>> affxparser? >>> >>> Best, >>> >>> Jim >>> >>> >>> -- >>> >>> James W. MacDonald, M.S. >>> Biostatistician >>> Affymetrix and cDNA Microarray Core >>> University of Michigan Cancer Center >>> 1500 E. Medical Center Drive >>> 7410 CCGC >>> Ann Arbor MI 48109 >>> 734-647-5623 >>> >>> >>> >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and >>> should not be used for urgent or sensitive issues. > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and > should not be used for urgent or sensitive issues.
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