annotation package for HuEx-1_0-st-v1 platform instead of pd.huex.1.0.st.v1
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@rahmatallah-yasir-6282
Last seen 8.1 years ago
I'm trying to combine some of the microarray CEL files from the GEO series GSE7792 into an AffyBatch object using command 'read.affy' from package 'simpleaffy'. This command worked for other CEL files with different platforms (such as hgu133plus2, hgu133a and hgu95av2). For CEL files from this series, the annotation of the genes is from the 'huex10stv1' chip (Annotation: huex10stv1). I could not find a bioconductor annotation package for it, so the AffyBatch object is listed as follows: > GSE7792batch AffyBatch object size of arrays=2560x2560 features (38 kb) cdf=HuEx-1_0-st-v1 (??? affyids) number of samples=58 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuEx-1_0-st-v1 Library - package huex10stv1cdf not installed Bioconductor - huex10stv1cdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) Bioconductor package 'pd.huex.1.0.st.v2' (Platform Design Info for Affymetrix HuEx-1_0-st-v2) is available, but the samples in GSE7792 seem to be old and require 'HuEx-1_0-st-v1' annotation instead. Is 'HuEx-1_0-st-v1' annotation available elsewhere or should the CEL samples themselves be handled differently? Your help is appreciated. Yasir Rahmatallah, Ph.D. Post Doctoral Fellow Division of Biomedical Informatics University of Arkansas for Medical Sciences (UAMS) Office: 501-526-7814 ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including a...{{dropped:10}}
Microarray Annotation hgu133a hgu133plus2 cdf Microarray Annotation hgu133a hgu133plus2 • 2.1k views
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cstrato ★ 3.9k
@cstrato-908
Last seen 4.0 years ago
Austria
For exon arrays you need to use either package oligo or package xps, see: http://www.bioconductor.org/help/workflows/arrays/ 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 12/10/13 6:54 PM, Rahmatallah, Yasir wrote: > I'm trying to combine some of the microarray CEL files from the GEO series GSE7792 into an AffyBatch object using command 'read.affy' from package 'simpleaffy'. This command worked for other CEL files with different platforms (such as hgu133plus2, hgu133a and hgu95av2). For CEL files from this series, the annotation of the genes is from the 'huex10stv1' chip (Annotation: huex10stv1). I could not find a bioconductor annotation package for it, so the AffyBatch object is listed as follows: > >> GSE7792batch > AffyBatch object > size of arrays=2560x2560 features (38 kb) > cdf=HuEx-1_0-st-v1 (??? affyids) > number of samples=58 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuEx-1_0-st-v1 > Library - package huex10stv1cdf not installed > Bioconductor - huex10stv1cdf not available > In addition: Warning message: > missing cdf environment! in show(AffyBatch) > > Bioconductor package 'pd.huex.1.0.st.v2' (Platform Design Info for Affymetrix HuEx-1_0-st-v2) is available, but the samples in GSE7792 seem to be old and require 'HuEx-1_0-st-v1' annotation instead. Is 'HuEx-1_0-st-v1' annotation available elsewhere or should the CEL samples themselves be handled differently? > Your help is appreciated. > > Yasir Rahmatallah, Ph.D. > Post Doctoral Fellow > Division of Biomedical Informatics > University of Arkansas for Medical Sciences (UAMS) > Office: 501-526-7814 > > ---------------------------------------------------------------------- > Confidentiality Notice: This e-mail message, including a...{{dropped:10}} > > _______________________________________________ > 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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