Quality Control of Exon arrays using xps?
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@achilleas-pitsillides-4316
Last seen 7.1 years ago
Hi all, I was was wondering what if there is an easy way to do evaluate QC (quality control) on exon arrays. For Gene arrays I used simpleAffy but that works only on an affybatch object. Thanks in advance, Achilleas [[alternative HTML version deleted]]
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cstrato ★ 3.9k
@cstrato-908
Last seen 3.0 years ago
Austria
Dear Achilleas, It depends what you are looking for. Currently xps supports hist() (or root.density()), boxplot (or root.profile()), nuseplot(), rleplot(). Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 12/20/10 5:44 PM, Achilleas Pitsillides wrote: > Hi all, > I was was wondering what if there is an easy way to do evaluate QC (quality > control) on exon arrays. > For Gene arrays I used simpleAffy but that works only on an affybatch > object. > > Thanks in advance, > Achilleas > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Dear Christian, Thanks for the prompt response and at the same time I apologize for my so late acknowledgement. One of the things that I am trying to do is check the some of the following pm_mean and bgrd_mean evaluated from the probes listed in the BGP file. I am just learning my way around the xps package but it seems that the BGP file information is not in the schemeTreeSet. In addition some times I need to view specific control probes and the way I go about that feels rather clunky (that's were my previous question about the description of the exonmask came in. For example to select the probes related to the polya_splike. I obtain the annotation frame find the UNIT_IDs that correspond to the polya_spike genename and then use the Mask info to get the corresponding X Y co-ordinates of the raw intensity values and then unravel those with something of the form Y*2560+X+1 to get the position in the intensity file. Is there a more direct way to do this? Thanks in advance, Achilleas On Mon, Dec 20, 2010 at 12:34 PM, cstrato <cstrato@aon.at> wrote: > Dear Achilleas, > > It depends what you are looking for. Currently xps supports hist() (or > root.density()), boxplot (or root.profile()), nuseplot(), rleplot(). > > Best regards > Christian > _._._._._._._._._._._._._._._._._._ > C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a > V.i.e.n.n.a A.u.s.t.r.i.a > e.m.a.i.l: cstrato at aon.at > _._._._._._._._._._._._._._._._._._ > > > > On 12/20/10 5:44 PM, Achilleas Pitsillides wrote: > >> Hi all, >> I was was wondering what if there is an easy way to do evaluate QC >> (quality >> control) on exon arrays. >> For Gene arrays I used simpleAffy but that works only on an affybatch >> object. >> >> Thanks in advance, >> Achilleas >> >> [[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 >> >> [[alternative HTML version deleted]]
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Dear Achilleas, I must admit that it is not quite clear to me what you want to do. What do you mean with BGP file? Do you mean the Affymetrix "*.bgp" file? This file is not necessary since it contains redundant information already present in the "*.pgf" file. What do you mean with bgrd_mean and pm_mean? The mask for genomic bgrd is -1 (32768) and for antigenomic bgrd -2 (65536). Using "export.scheme()" you can extract the information from the different scheme trees, see "?validTreetype", e.g. the "*.scm" tree contains the (x,y) coordinates and mask for the UNIT_ID and PROBESET_ID. I am not sure if this answers your question. Best regards Christian On 12/22/10 9:32 PM, Achilleas Pitsillides wrote: > Dear Christian, > Thanks for the prompt response and at the same time I apologize for my so > late acknowledgement. One of the things that I am trying to do is check the > some of the following pm_mean and bgrd_mean evaluated from the probes listed > in the BGP file. I am just learning my way around the xps package but it > seems that the BGP file information is not in the schemeTreeSet. In addition > some times I need to view specific control probes and the way I go about > that feels rather clunky (that's were my previous question about the > description of the exonmask came in. For example to select the probes > related to the polya_splike. I obtain the annotation frame find the UNIT_IDs > that correspond to the polya_spike genename and then use the Mask info to > get the corresponding X Y co-ordinates of the raw intensity values and then > unravel those with something of the form Y*2560+X+1 to get the position in > the intensity file. Is there a more direct way to do this? > > Thanks in advance, > Achilleas > > On Mon, Dec 20, 2010 at 12:34 PM, cstrato<cstrato at="" aon.at=""> wrote: > >> Dear Achilleas, >> >> It depends what you are looking for. Currently xps supports hist() (or >> root.density()), boxplot (or root.profile()), nuseplot(), rleplot(). >> >> Best regards >> Christian >> _._._._._._._._._._._._._._._._._._ >> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a >> V.i.e.n.n.a A.u.s.t.r.i.a >> e.m.a.i.l: cstrato at aon.at >> _._._._._._._._._._._._._._._._._._ >> >> >> >> On 12/20/10 5:44 PM, Achilleas Pitsillides wrote: >> >>> Hi all, >>> I was was wondering what if there is an easy way to do evaluate QC >>> (quality >>> control) on exon arrays. >>> For Gene arrays I used simpleAffy but that works only on an affybatch >>> object. >>> >>> Thanks in advance, >>> Achilleas >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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