errors in FRMA
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@mayte-suarez-farinas-2068
Last seen 6.6 years ago
United States
Hi all, I have been trying to use frma in hgu133a2 and hgu133aplus2 chips for the last 2 days unsuccessfully. I used to be able to do so with previous versions using hgu133plus2ASaFrma functions, but a call on either functions hgu133plus2ASaFrma or hgu133a2ASaFrma produce the following result Error: could not find function "hgu133plus2ASaFrma" I tried to use then the function convertPlatform and it produces a new AffyBatch with hgu133a annotation but a call to frma(newAffyBatch) frizzes R. When I tried to see why I discovered that the new AffyBatch has NA in the intensity slot. Thanks in advance!! Mayte Suarez-Farinas Research Assistant Professor, Laboratory of Investigative Dermatology Biostatistician, Center for Clinical and Translational Science The Rockefeller University 1230 York Ave, Box 178, New York, NY, 10065 Phone: +1(212) 327-8213 Fax: +1(212) 327-8232
Annotation hgu133a2 hgu133a frma Annotation hgu133a2 hgu133a frma • 878 views
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@matthew-mccall-4459
Last seen 2.5 years ago
United States
Mayte, Do you mean you are trying to preprocess hgu133a2 and hgu133plus2 chips together? I wouldn't recommend this -- probe behavior (even for identical probes) seems to differ between the 2 platforms quite a bit. As for the hguXXXASXXFrma functions, these were replaced by convertPlatform (for the rare cases in which one might want to preprocess one platform as if it were really a different platform). This is mostly for special cases like hgu133atag and hgu133a, which differ by just a handful of probesets. If you provide an example (with sessionInfo), I can look into why convertPlatform might be failing. Best, Matt On Sat, Apr 28, 2012 at 9:28 AM, Mayte Suarez-Farinas <farinam at="" mail.rockefeller.edu=""> wrote: > Hi all, > > I have been trying to use frma in hgu133a2 and hgu133aplus2 chips for the last 2 days unsuccessfully. I used to be able to do so with previous versions using hgu133plus2ASaFrma functions, but a call on either ?functions hgu133plus2ASaFrma or hgu133a2ASaFrma produce the following result > > Error: could not find function "hgu133plus2ASaFrma" > > I tried to use then the function convertPlatform and it produces a new AffyBatch with hgu133a annotation but a call to frma(newAffyBatch) ?frizzes R. When I tried to see why I discovered that the new AffyBatch has NA in the intensity slot. > > Thanks in advance!! > > Mayte Suarez-Farinas > Research Assistant Professor, ?Laboratory of Investigative Dermatology > Biostatistician, ?Center for Clinical and Translational Science > The Rockefeller University > 1230 York Ave, Box 178, > New York, NY, 10065 > Phone: +1(212) 327-8213 > Fax: ? ? ?+1(212) 327-8232 > > _______________________________________________ > 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 -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880
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Thanks Matthew, I am trying to preprocess two batches, hgu133a2 and hgu133plus2 separately using frma but I want to then subset for the set of common probes, that's why I want to frma hgu133plus2 chips to hgu133a anyway, I try the convertPlatform but as I said it did not work out. DO you me to send you affybatch ? Txs Mayte Suarez-Farinas Research Assistant Professor, Laboratory of Investigative Dermatology Biostatistician, Center for Clinical and Translational Science The Rockefeller University 1230 York Ave, Box 178, New York, NY, 10065 Phone: +1(212) 327-8213 Fax: +1(212) 327-8232 On Apr 28, 2012, at 3:38 PM, Matthew McCall wrote: > Mayte, > > Do you mean you are trying to preprocess hgu133a2 and hgu133plus2 > chips together? I wouldn't recommend this -- probe behavior (even for > identical probes) seems to differ between the 2 platforms quite a bit. > > As for the hguXXXASXXFrma functions, these were replaced by > convertPlatform (for the rare cases in which one might want to > preprocess one platform as if it were really a different platform). > This is mostly for special cases like hgu133atag and hgu133a, which > differ by just a handful of probesets. > > If you provide an example (with sessionInfo), I can look into why > convertPlatform might be failing. > > Best, > Matt > > On Sat, Apr 28, 2012 at 9:28 AM, Mayte Suarez-Farinas > <farinam at="" mail.rockefeller.edu=""> wrote: >> Hi all, >> >> I have been trying to use frma in hgu133a2 and hgu133aplus2 chips for the last 2 days unsuccessfully. I used to be able to do so with previous versions using hgu133plus2ASaFrma functions, but a call on either functions hgu133plus2ASaFrma or hgu133a2ASaFrma produce the following result >> >> Error: could not find function "hgu133plus2ASaFrma" >> >> I tried to use then the function convertPlatform and it produces a new AffyBatch with hgu133a annotation but a call to frma(newAffyBatch) frizzes R. When I tried to see why I discovered that the new AffyBatch has NA in the intensity slot. >> >> Thanks in advance!! >> >> Mayte Suarez-Farinas >> Research Assistant Professor, Laboratory of Investigative Dermatology >> Biostatistician, Center for Clinical and Translational Science >> The Rockefeller University >> 1230 York Ave, Box 178, >> New York, NY, 10065 >> Phone: +1(212) 327-8213 >> Fax: +1(212) 327-8232 >> >> _______________________________________________ >> 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 > > > > -- > Matthew N McCall, PhD > 112 Arvine Heights > Rochester, NY 14611 > Cell: 202-222-5880
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Mayte, You don't need to send me a data object just your R script and your sessionInfo. Then I can try to reproduce the error you're getting. Matt On Sat, Apr 28, 2012 at 3:51 PM, Mayte Suarez-Farinas <farinam at="" mail.rockefeller.edu=""> wrote: > Thanks Matthew, > > I am trying to preprocess two batches, hgu133a2 and hgu133plus2 separately using frma but I want to > then subset for the set of common probes, that's why I want to frma hgu133plus2 chips to hgu133a anyway, > I try the convertPlatform but as I said it did not work out. DO you me to send you ?affybatch ? > ?Txs > Mayte Suarez-Farinas > Research Assistant Professor, ?Laboratory of Investigative Dermatology > Biostatistician, ?Center for Clinical and Translational Science > The Rockefeller University > 1230 York Ave, Box 178, > New York, NY, 10065 > Phone: +1(212) 327-8213 > Fax: ? ? ?+1(212) 327-8232 > > > > > > > > > > > On Apr 28, 2012, at 3:38 PM, Matthew McCall wrote: > >> Mayte, >> >> Do you mean you are trying to preprocess hgu133a2 and hgu133plus2 >> chips together? I wouldn't recommend this -- probe behavior (even for >> identical probes) seems to differ between the 2 platforms quite a bit. >> >> As for the hguXXXASXXFrma functions, these were replaced by >> convertPlatform (for the rare cases in which one might want to >> preprocess one platform as if it were really a different platform). >> This is mostly for special cases like hgu133atag and hgu133a, which >> differ by just a handful of probesets. >> >> If you provide an example (with sessionInfo), I can look into why >> convertPlatform might be failing. >> >> Best, >> Matt >> >> On Sat, Apr 28, 2012 at 9:28 AM, Mayte Suarez-Farinas >> <farinam at="" mail.rockefeller.edu=""> wrote: >>> Hi all, >>> >>> I have been trying to use frma in hgu133a2 and hgu133aplus2 chips for the last 2 days unsuccessfully. I used to be able to do so with previous versions using hgu133plus2ASaFrma functions, but a call on either ?functions hgu133plus2ASaFrma or hgu133a2ASaFrma produce the following result >>> >>> Error: could not find function "hgu133plus2ASaFrma" >>> >>> I tried to use then the function convertPlatform and it produces a new AffyBatch with hgu133a annotation but a call to frma(newAffyBatch) ?frizzes R. When I tried to see why I discovered that the new AffyBatch has NA in the intensity slot. >>> >>> Thanks in advance!! >>> >>> Mayte Suarez-Farinas >>> Research Assistant Professor, ?Laboratory of Investigative Dermatology >>> Biostatistician, ?Center for Clinical and Translational Science >>> The Rockefeller University >>> 1230 York Ave, Box 178, >>> New York, NY, 10065 >>> Phone: +1(212) 327-8213 >>> Fax: ? ? ?+1(212) 327-8232 >>> >>> _______________________________________________ >>> 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 >> >> >> >> -- >> Matthew N McCall, PhD >> 112 Arvine Heights >> Rochester, NY 14611 >> Cell: 202-222-5880 > -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880
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>annotation(object) [1] "hgu133plus2" >new.object<-convertPlatform(object,'hgu133a') Loading required package: hgu133aprobe Loading required package: hgu133plus2probe Attaching package: ?hgu133plus2cdf? The following object(s) are masked from ?package:hgu133acdf?: i2xy, xy2i head(intensity(new.object)) 1 2 3 4 5 6 7 8 9 10 1 NA NA NA NA NA NA NA NA NA NA 2 NA NA NA NA NA NA NA NA NA NA 3 NA NA NA NA NA NA NA NA NA NA 4 NA NA NA NA NA NA NA NA NA NA 5 NA NA NA NA NA NA NA NA NA NA 6 NA NA NA NA NA NA NA NA NA NA sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines grid stats graphics grDevices utils datasets methods base other attached packages: [1] frmaTools_1.6.0 preprocessCore_1.16.0 a4_1.2.0 a4Reporting_1.2.0 a4Classif_1.2.0 [6] varSelRF_0.7-3 randomForest_4.6-6 pamr_1.54 survival_2.36-12 ROCR_1.0-4 [11] MLInterfaces_1.34.2 sfsmisc_1.0-19 cluster_1.14.2 rda_1.0.2 rpart_3.1-52 [16] a4Base_1.2.3 a4Core_1.2.0 a4Preproc_1.2.0 glmnet_1.7.3 Matrix_1.0-4 [21] multtest_2.10.0 mpm_1.0-22 MASS_7.3-17 annaffy_1.26.0 gplots_2.10.1 [26] KernSmooth_2.23-7 caTools_1.12 bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2 [31] limma_3.10.3 annotate_1.32.1 simpleaffy_2.30.0 genefilter_1.36.0 lattice_0.20-0 [36] gcrma_2.26.0 arrayQualityMetrics_3.10.0 affycoretools_1.26.0 KEGG.db_2.6.1 GO.db_2.6.1 [41] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.16.19 affy_1.32.1 Biobase_2.14.0 loaded via a namespace (and not attached): [1] affyio_1.22.0 affyPLM_1.30.0 beadarray_2.4.2 BiocInstaller_1.2.1 biomaRt_2.10.0 Biostrings_2.22.0 Cairo_1.5-1 [8] Category_2.20.0 colorspace_1.1-1 GOstats_2.20.0 graph_1.32.0 GSEABase_1.16.1 Hmisc_3.9-2 hwriter_1.3 [15] IRanges_1.12.6 latticeExtra_0.6-19 mboost_2.1-2 plyr_1.7.1 RBGL_1.30.1 RColorBrewer_1.0-5 RCurl_1.91-1 [22] reshape2_1.2.1 setRNG_2009.11-1 stringr_0.6 SVGAnnotation_0.9-0 tools_2.14.1 vsn_3.22.0 XML_3.9-4 [29] xtable_1.7-0 zlibbioc_1.0.1 Mayte Suarez-Farinas Research Assistant Professor, Laboratory of Investigative Dermatology Biostatistician, Center for Clinical and Translational Science The Rockefeller University 1230 York Ave, Box 178, New York, NY, 10065 Phone: +1(212) 327-8213 Fax: +1(212) 327-8232 On Apr 28, 2012, at 3:55 PM, Matthew McCall wrote: > sessionInfo
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