Empty featureData in ExpressionSet generated by affy::justRMA
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David Shih ▴ 30
@david-shih-4653
Last seen 9.6 years ago
Dear list, I am using the affy package to normalize expression data on the HT Human Genome U133A platform. According to earlier posting on the list, this is equivalent to U133Av2. I used the justRMA() function to normalize the data, and obtained an ExpressionSet object with an empty featureData slot. I understand that I can retrive the annotation information from: library(hgu133a2.db) However, I am uncertain whether the probes in the annotation library are in the same order as the ExpressionSet object. Can I add the probe IDs using the following code? library(hgu133a2.db) keys <- mappedkeys(hgu133ai2ACCNUM); expr <- exprs(eset); rownames(expr) <- keys; Best regards, David Shih, Graduate Student The Hospital for Sick Children Brain Tumour Research Centre 101 College Street, TMDT-11-401M Toronto, ON M5G1L7 Canada Tel: 416-813-7654 x4327 > sessionInfo() R version 2.12.2 (2011-02-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 RSQLite_0.9-4 [4] DBI_0.2-5 AnnotationDbi_1.12.0 hthgu133acdf_2.7.0 [7] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.2
Annotation hgu133a2 probe affy Annotation hgu133a2 probe affy • 1.2k views
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@james-w-macdonald-5106
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Hi David, On 5/18/2011 1:31 PM, David Shih wrote: > Dear list, > > I am using the affy package to normalize expression data on the HT > Human Genome U133A platform. According to earlier posting on the list, > this is equivalent to U133Av2. > > I used the justRMA() function to normalize the data, and obtained an > ExpressionSet object with an empty featureData slot. You may be misunderstanding the purpose of the featureData slot. According to ?eSet-class: 'featureData': Contains variables describing features (i.e., rows in 'assayData') unique to this experiment. Use the 'annotation' slot to efficiently reference feature data common to the annotation package used in the experiment. Class: 'AnnotatedDataFrame-class' The probeset IDs are not unique to any particular experiment, so are stored as part of the assayData, which can be extracted using e.g., exprs(): > data(sample.ExpressionSet) > head(exprs(sample.ExpressionSet)) A B C D E F G AFFX-MurIL2_at 192.7420 85.75330 176.7570 135.5750 64.49390 76.3569 160.5050 AFFX-MurIL10_at 97.1370 126.19600 77.9216 93.3713 24.39860 85.5088 98.9086 AFFX-MurIL4_at 45.8192 8.83135 33.0632 28.7072 5.94492 28.2925 30.9694 AFFX-MurFAS_at 22.5445 3.60093 14.6883 12.3397 36.86630 11.2568 23.0034 AFFX-BioB-5_at 96.7875 30.43800 46.1271 70.9319 56.17440 42.6756 86.5156 AFFX-BioB-M_at 89.0730 25.84610 57.2033 69.9766 49.58220 26.1262 75.0083 Best, Jim > > I understand that I can retrive the annotation information from: > library(hgu133a2.db) > > However, I am uncertain whether the probes in the annotation library > are in the same order as the ExpressionSet object. > > Can I add the probe IDs using the following code? > > library(hgu133a2.db) > keys<- mappedkeys(hgu133ai2ACCNUM); > expr<- exprs(eset); > rownames(expr)<- keys; > > > Best regards, > > David Shih, Graduate Student > The Hospital for Sick Children > Brain Tumour Research Centre > 101 College Street, TMDT-11-401M > Toronto, ON M5G1L7 > Canada > Tel: 416-813-7654 x4327 > > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 RSQLite_0.9-4 > [4] DBI_0.2-5 AnnotationDbi_1.12.0 hthgu133acdf_2.7.0 > [7] affy_1.28.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.2 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** 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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Hi Jim, Thank you for clarifying the purpose of the featureData slot. The assayData slot also appears empty in my ExpressionSet. The rownames are missing in my expression matrix extracted using. > exprs(eset) I was hoping to fill the rownames of my matrix using keys obtained from > keys <- mappedkeys(hgu133a2ACCUM) I checked that all the keys are mapped, and I am under the impression that they should be for hgu133a2ACCUM. My main concern is that hgu133a2ACCUM may not return the keys (probe ids) in the same order as they appear in the expression matrix, which would cause the probes to be incorrectly mapped. I have no problem with normalizing older platforms like U133. All the probe ids are automatically assigned upon extraction with exprs(). However, the hthgu133a platform does not appear to be as straightforward. I had a similar problems with the HT Human Gene 1.0 ST platform. I ended up using the oligo package, whicih provides a getNetAffx() function to retrieve probe annotation data. However, the existing normalization code precludes from switching to the oligo package. Best regards, David On Wed, May 18, 2011 at 01:51:01PM -0400, James W. MacDonald wrote: > Hi David, > > On 5/18/2011 1:31 PM, David Shih wrote: > >Dear list, > > > >I am using the affy package to normalize expression data on the HT > >Human Genome U133A platform. According to earlier posting on the list, > >this is equivalent to U133Av2. > > > >I used the justRMA() function to normalize the data, and obtained an > >ExpressionSet object with an empty featureData slot. > > You may be misunderstanding the purpose of the featureData slot. > According to ?eSet-class: > > 'featureData': Contains variables describing features (i.e., rows > in 'assayData') unique to this experiment. Use the > 'annotation' slot to efficiently reference feature data > common to the annotation package used in the experiment. > Class: 'AnnotatedDataFrame-class' > > The probeset IDs are not unique to any particular experiment, so are > stored as part of the assayData, which can be extracted using e.g., > exprs(): > > > data(sample.ExpressionSet) > > head(exprs(sample.ExpressionSet)) > A B C D E > F G > AFFX-MurIL2_at 192.7420 85.75330 176.7570 135.5750 64.49390 > 76.3569 160.5050 > AFFX-MurIL10_at 97.1370 126.19600 77.9216 93.3713 24.39860 > 85.5088 98.9086 > AFFX-MurIL4_at 45.8192 8.83135 33.0632 28.7072 5.94492 > 28.2925 30.9694 > AFFX-MurFAS_at 22.5445 3.60093 14.6883 12.3397 36.86630 > 11.2568 23.0034 > AFFX-BioB-5_at 96.7875 30.43800 46.1271 70.9319 56.17440 > 42.6756 86.5156 > AFFX-BioB-M_at 89.0730 25.84610 57.2033 69.9766 49.58220 > 26.1262 75.0083 > > Best, > > Jim > > > > > >I understand that I can retrive the annotation information from: > >library(hgu133a2.db) > > > >However, I am uncertain whether the probes in the annotation library > >are in the same order as the ExpressionSet object. > > > >Can I add the probe IDs using the following code? > > > >library(hgu133a2.db) > >keys<- mappedkeys(hgu133ai2ACCNUM); > >expr<- exprs(eset); > >rownames(expr)<- keys; > > > > > >Best regards, > > > >David Shih, Graduate Student > >The Hospital for Sick Children > >Brain Tumour Research Centre > >101 College Street, TMDT-11-401M > >Toronto, ON M5G1L7 > >Canada > >Tel: 416-813-7654 x4327 > > > > > >>sessionInfo() > >R version 2.12.2 (2011-02-25) > >Platform: x86_64-unknown-linux-gnu (64-bit) > > > >locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > >[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > >attached base packages: > >[1] stats graphics grDevices utils datasets methods base > > > >other attached packages: > >[1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 RSQLite_0.9-4 > >[4] DBI_0.2-5 AnnotationDbi_1.12.0 hthgu133acdf_2.7.0 > >[7] affy_1.28.0 Biobase_2.10.0 > > > >loaded via a namespace (and not attached): > >[1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.2 > > > >_______________________________________________ > >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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > 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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Hi David, On 5/18/2011 2:04 PM, David Shih wrote: > Hi Jim, > > Thank you for clarifying the purpose of the featureData slot. > The assayData slot also appears empty in my ExpressionSet. It's not empty, you just didn't access it correctly. > showMethods(exprs, class="ExpressionSet", includeDefs = TRUE) Function: exprs (package Biobase) object="ExpressionSet" function (object) assayDataElement(object, "exprs") and > assayDataElement function (object, elt) assayData(object)[[elt]] <environment: namespace:biobase=""> So exprs() is extracting data from your assayData slot, but you have to choose the "exprs" element of the AssayData object that assayData() returns. > > The rownames are missing in my expression matrix extracted using. >> exprs(eset) Well, they *should* be there, so this indicates some bug in the processing. What does exprs(eset)[1:5,1:5} look like, exactly? Best, Jim > > I was hoping to fill the rownames of my matrix using keys obtained > from >> keys<- mappedkeys(hgu133a2ACCUM) > > I checked that all the keys are mapped, and I am under the impression > that they should be for hgu133a2ACCUM. > > My main concern is that hgu133a2ACCUM may not return the keys > (probe ids) in the same order as they appear in the expression matrix, > which would cause the probes to be incorrectly mapped. > > I have no problem with normalizing older platforms like U133. All the > probe ids are automatically assigned upon extraction with exprs(). > However, the hthgu133a platform does not appear to be as > straightforward. > > I had a similar problems with the HT Human Gene 1.0 ST platform. > I ended up using the oligo package, whicih provides a getNetAffx() > function to retrieve probe annotation data. > However, the existing normalization code precludes from switching to > the oligo package. > > Best regards, > David > > On Wed, May 18, 2011 at 01:51:01PM -0400, James W. MacDonald wrote: >> Hi David, >> >> On 5/18/2011 1:31 PM, David Shih wrote: >>> Dear list, >>> >>> I am using the affy package to normalize expression data on the HT >>> Human Genome U133A platform. According to earlier posting on the list, >>> this is equivalent to U133Av2. >>> >>> I used the justRMA() function to normalize the data, and obtained an >>> ExpressionSet object with an empty featureData slot. >> >> You may be misunderstanding the purpose of the featureData slot. >> According to ?eSet-class: >> >> 'featureData': Contains variables describing features (i.e., rows >> in 'assayData') unique to this experiment. Use the >> 'annotation' slot to efficiently reference feature data >> common to the annotation package used in the experiment. >> Class: 'AnnotatedDataFrame-class' >> >> The probeset IDs are not unique to any particular experiment, so are >> stored as part of the assayData, which can be extracted using e.g., >> exprs(): >> >>> data(sample.ExpressionSet) >>> head(exprs(sample.ExpressionSet)) >> A B C D E >> F G >> AFFX-MurIL2_at 192.7420 85.75330 176.7570 135.5750 64.49390 >> 76.3569 160.5050 >> AFFX-MurIL10_at 97.1370 126.19600 77.9216 93.3713 24.39860 >> 85.5088 98.9086 >> AFFX-MurIL4_at 45.8192 8.83135 33.0632 28.7072 5.94492 >> 28.2925 30.9694 >> AFFX-MurFAS_at 22.5445 3.60093 14.6883 12.3397 36.86630 >> 11.2568 23.0034 >> AFFX-BioB-5_at 96.7875 30.43800 46.1271 70.9319 56.17440 >> 42.6756 86.5156 >> AFFX-BioB-M_at 89.0730 25.84610 57.2033 69.9766 49.58220 >> 26.1262 75.0083 >> >> Best, >> >> Jim >> >> >>> >>> I understand that I can retrive the annotation information from: >>> library(hgu133a2.db) >>> >>> However, I am uncertain whether the probes in the annotation library >>> are in the same order as the ExpressionSet object. >>> >>> Can I add the probe IDs using the following code? >>> >>> library(hgu133a2.db) >>> keys<- mappedkeys(hgu133ai2ACCNUM); >>> expr<- exprs(eset); >>> rownames(expr)<- keys; >>> >>> >>> Best regards, >>> >>> David Shih, Graduate Student >>> The Hospital for Sick Children >>> Brain Tumour Research Centre >>> 101 College Street, TMDT-11-401M >>> Toronto, ON M5G1L7 >>> Canada >>> Tel: 416-813-7654 x4327 >>> >>> >>>> sessionInfo() >>> R version 2.12.2 (2011-02-25) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 RSQLite_0.9-4 >>> [4] DBI_0.2-5 AnnotationDbi_1.12.0 hthgu133acdf_2.7.0 >>> [7] affy_1.28.0 Biobase_2.10.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.2 >>> >>> _______________________________________________ >>> 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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** 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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Hi Jim, It turns out that the assayData slot was not filled during the post-processing normalization. The original ExpressionSet object returned by justRMA() correctly populates the assayData slot. > exprs(eset)[1:5, 1:5] 5500024024214122006605.A01.CEL 5500024024214122006605.A02.CEL 1007_s_at 9.261711 9.672637 1053_at 5.732471 7.267763 117_at 5.316724 4.759532 121_at 6.999956 6.848935 1255_g_at 4.614048 4.572704 5500024024214122006605.A03.CEL 5500024024214122006605.A05.CEL 1007_s_at 9.780707 9.684070 1053_at 8.433437 7.870544 117_at 4.760007 4.783464 121_at 6.647044 6.635504 1255_g_at 4.577906 4.548474 5500024024214122006605.A06.CEL 1007_s_at 9.384182 1053_at 7.388526 117_at 5.662874 121_at 6.433151 1255_g_at 4.640982 I'll have to update the post-processing normalization script to reconstruct the ExpressionSet object properly. On another note, it seems that the probe ids in the expression matrix returned by exprs() are largely in the same order as the keys returned by mappedkeys(hgu133a2ACCNUM): > keys <- mappedkeys(hgu133a2ACCNUM); > probes <- rownames(exprs(eset)); > length(probes) [1] 22277 > length(keys) [1] 22277 > sum(probes == keys) [1] 22230 > probes[probes != keys] [1] "AFFX-hum_alu_at" "AFFX-HUMGAPDH/M33197_3_at" [3] "AFFX-HUMGAPDH/M33197_5_at" "AFFX-HUMGAPDH/M33197_M_at" [5] "AFFX-HUMISGF3A/M97935_3_at" "AFFX-HUMISGF3A/M97935_5_at" [7] "AFFX-HUMISGF3A/M97935_MA_at" "AFFX-HUMISGF3A/M97935_MB_at" [9] "AFFX-HUMRGE/M10098_3_at" "AFFX-HUMRGE/M10098_5_at" [11] "AFFX-HUMRGE/M10098_M_at" "AFFX-LysX-3_at" [13] "AFFX-LysX-5_at" "AFFX-LysX-M_at" [15] "AFFX-M27830_3_at" "AFFX-M27830_5_at" [17] "AFFX-M27830_M_at" "AFFX-PheX-3_at" [19] "AFFX-PheX-5_at" "AFFX-PheX-M_at" [21] "AFFX-r2-Bs-dap-3_at" "AFFX-r2-Bs-dap-5_at" [23] "AFFX-r2-Bs-dap-M_at" "AFFX-r2-Bs-lys-3_at" [25] "AFFX-r2-Bs-lys-5_at" "AFFX-r2-Bs-lys-M_at" [27] "AFFX-r2-Bs-phe-3_at" "AFFX-r2-Bs-phe-5_at" [29] "AFFX-r2-Bs-phe-M_at" "AFFX-r2-Bs-thr-3_s_at" [31] "AFFX-r2-Bs-thr-5_s_at" "AFFX-r2-Bs-thr-M_s_at" [33] "AFFX-r2-Ec-bioB-3_at" "AFFX-r2-Ec-bioB-5_at" [35] "AFFX-r2-Ec-bioB-M_at" "AFFX-r2-Ec-bioC-3_at" [37] "AFFX-r2-Ec-bioC-5_at" "AFFX-r2-Ec-bioD-3_at" [39] "AFFX-r2-Ec-bioD-5_at" "AFFX-r2-P1-cre-3_at" [41] "AFFX-r2-P1-cre-5_at" "AFFX-ThrX-3_at" [43] "AFFX-ThrX-5_at" "AFFX-ThrX-M_at" [45] "AFFX-TrpnX-3_at" "AFFX-TrpnX-5_at" [47] "AFFX-TrpnX-M_at" The orders are the same, except that the order of the some control probes have changed. But I guess this match is not guaranteed to be true in general. Thank you for you help. Regards, David On Thu, May 19, 2011 at 09:55:51AM -0400, James W. MacDonald wrote: > Hi David, > > On 5/18/2011 2:04 PM, David Shih wrote: > >Hi Jim, > > > >Thank you for clarifying the purpose of the featureData slot. > >The assayData slot also appears empty in my ExpressionSet. > > It's not empty, you just didn't access it correctly. > > > showMethods(exprs, class="ExpressionSet", includeDefs = TRUE) > Function: exprs (package Biobase) > object="ExpressionSet" > function (object) > assayDataElement(object, "exprs") > > and > > > assayDataElement > function (object, elt) > assayData(object)[[elt]] > <environment: namespace:biobase=""> > > So exprs() is extracting data from your assayData slot, but you have > to choose the "exprs" element of the AssayData object that > assayData() returns. > > > > >The rownames are missing in my expression matrix extracted using. > >>exprs(eset) > > Well, they *should* be there, so this indicates some bug in the > processing. What does exprs(eset)[1:5,1:5} look like, exactly? > > Best, > > Jim > > > > > >I was hoping to fill the rownames of my matrix using keys obtained > >from > >>keys<- mappedkeys(hgu133a2ACCUM) > > > >I checked that all the keys are mapped, and I am under the impression > >that they should be for hgu133a2ACCUM. > > > >My main concern is that hgu133a2ACCUM may not return the keys > >(probe ids) in the same order as they appear in the expression matrix, > >which would cause the probes to be incorrectly mapped. > > > >I have no problem with normalizing older platforms like U133. All the > >probe ids are automatically assigned upon extraction with exprs(). > >However, the hthgu133a platform does not appear to be as > >straightforward. > > > >I had a similar problems with the HT Human Gene 1.0 ST platform. > >I ended up using the oligo package, whicih provides a getNetAffx() > >function to retrieve probe annotation data. > >However, the existing normalization code precludes from switching to > >the oligo package. > > > >Best regards, > >David > > > >On Wed, May 18, 2011 at 01:51:01PM -0400, James W. MacDonald wrote: > >>Hi David, > >> > >>On 5/18/2011 1:31 PM, David Shih wrote: > >>>Dear list, > >>> > >>>I am using the affy package to normalize expression data on the HT > >>>Human Genome U133A platform. According to earlier posting on the list, > >>>this is equivalent to U133Av2. > >>> > >>>I used the justRMA() function to normalize the data, and obtained an > >>>ExpressionSet object with an empty featureData slot. > >> > >>You may be misunderstanding the purpose of the featureData slot. > >>According to ?eSet-class: > >> > >>'featureData': Contains variables describing features (i.e., rows > >> in 'assayData') unique to this experiment. Use the > >> 'annotation' slot to efficiently reference feature data > >> common to the annotation package used in the experiment. > >> Class: 'AnnotatedDataFrame-class' > >> > >>The probeset IDs are not unique to any particular experiment, so are > >>stored as part of the assayData, which can be extracted using e.g., > >>exprs(): > >> > >>>data(sample.ExpressionSet) > >>>head(exprs(sample.ExpressionSet)) > >> A B C D E > >>F G > >>AFFX-MurIL2_at 192.7420 85.75330 176.7570 135.5750 64.49390 > >>76.3569 160.5050 > >>AFFX-MurIL10_at 97.1370 126.19600 77.9216 93.3713 24.39860 > >>85.5088 98.9086 > >>AFFX-MurIL4_at 45.8192 8.83135 33.0632 28.7072 5.94492 > >>28.2925 30.9694 > >>AFFX-MurFAS_at 22.5445 3.60093 14.6883 12.3397 36.86630 > >>11.2568 23.0034 > >>AFFX-BioB-5_at 96.7875 30.43800 46.1271 70.9319 56.17440 > >>42.6756 86.5156 > >>AFFX-BioB-M_at 89.0730 25.84610 57.2033 69.9766 49.58220 > >>26.1262 75.0083 > >> > >>Best, > >> > >>Jim > >> > >> > >>> > >>>I understand that I can retrive the annotation information from: > >>>library(hgu133a2.db) > >>> > >>>However, I am uncertain whether the probes in the annotation library > >>>are in the same order as the ExpressionSet object. > >>> > >>>Can I add the probe IDs using the following code? > >>> > >>>library(hgu133a2.db) > >>>keys<- mappedkeys(hgu133ai2ACCNUM); > >>>expr<- exprs(eset); > >>>rownames(expr)<- keys; > >>> > >>> > >>>Best regards, > >>> > >>>David Shih, Graduate Student > >>>The Hospital for Sick Children > >>>Brain Tumour Research Centre > >>>101 College Street, TMDT-11-401M > >>>Toronto, ON M5G1L7 > >>>Canada > >>>Tel: 416-813-7654 x4327 > >>> > >>> > >>>>sessionInfo() > >>>R version 2.12.2 (2011-02-25) > >>>Platform: x86_64-unknown-linux-gnu (64-bit) > >>> > >>>locale: > >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > >>> [9] LC_ADDRESS=C LC_TELEPHONE=C > >>>[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > >>> > >>>attached base packages: > >>>[1] stats graphics grDevices utils datasets methods base > >>> > >>>other attached packages: > >>>[1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 RSQLite_0.9-4 > >>>[4] DBI_0.2-5 AnnotationDbi_1.12.0 hthgu133acdf_2.7.0 > >>>[7] affy_1.28.0 Biobase_2.10.0 > >>> > >>>loaded via a namespace (and not attached): > >>>[1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.2 > >>> > >>>_______________________________________________ > >>>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 > >> > >>-- > >>James W. MacDonald, M.S. > >>Biostatistician > >>Douglas Lab > >>University of Michigan > >>Department of Human Genetics > >>5912 Buhl > >>1241 E. Catherine St. > >>Ann Arbor MI 48109-5618 > >>734-615-7826 > >>********************************************************** > >>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 > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > 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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