I'm using the Biobase package to build an ExpressionSet from scratch using data from a custom 8x15k Agilent microarray. I'm getting this error and can't quite figure it out. Does anyone know how *phenoData* can extend the * annotation*? I would like to connect *phenoData* to *exprs* with the Chip and Block numbers, somehow, but I don't know how to do this. Any help would be greatly appreciated! > sponge_ExpressionSet<-new("ExpressionSet",exprs=sponge_data,phenoDat a=samples_matrix,experimentData=experimentData,annotation=annotation_m atrix)Error: ExpressionSet 'phenoData' is class 'matrix' but should be or extend 'AnnotatedDataFrame' Details: These are the instructions that I am following: http://www.bioconductor.org/help/course- materials/2006/biocintro_oct/labs/ExpressionSet/ExpressionSetIntro- lab.pdf http://www.bioconductor.org/packages/2.13/bioc/vignettes/Biobase/inst/ doc/ExpressionSetIntroduction.pdf 1. *exprs* data (sponge_data) were extracted from GenePix *.gpr files and are in a 15744 x 72 double matrix with RefNumber as rownames: > head(sponge_data) Block 1 Chip 1 Block 2 Chip 1 Block 3 Chip 1 Block 4 Chip 1 Block 5 Chip 1 15744 2 23 6 9 3 15580 9 16 11 11 6 15416 1 0 0 0 1 15252 1 0 0 -1 0 15088 3 2 0 1 0 14924 0 -1 0 0 1 2. *phenoData* (samples_matrix) is a 72 x 8 character matrix with experimental design variables for each chip and block: > head(samples_matrix) Chip Number File Name Hyb Date Tank Treatment Colony Raceway [1,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "C3" "UC" "P" "B" [2,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "B2" "UD" "P" "A" [3,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "B2" "UD" "O" "A" [4,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "D3" "OD" "BL" "A" [5,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "D1" "OD" "O" "B" [6,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "C3" "UC" "O" "B" > all(rownames(samples_matrix)==colnames(sponge_data))[1] TRUE 3. *annotation* is (annotation_matrix) is a 15744 x 23 character matrix with microarray annotation info, including RefNumber: > head(annotation_matrix) Column Row RefNumber Name Append Name [1,] "96" "164" " 1" "GE_BrightCorner" "GE_BrightCorner" [2,] "96" "162" " 2" "DarkCorner" "DarkCorner" [3,] "96" "160" " 3" "DarkCorner" "DarkCorner" [4,] "96" "158" " 4" "222803147_EZ031535.1" "222803147_EZ031535.1_16-465" [5,] "96" "156" " 5" "222546129_EZ002319.1" "222546129_EZ002319.1_1845-2030" [6,] "96" "154" " 6" "222801996_EZ030384.1" "222801996_EZ030384.1_31-2558" > all(rownames(annotation_matrix)==rownames(sponge_data))[1] TRUE 4. experimentData (experimentData): metadata info But, when I go to finally assemble the ExpressionSet, the error below occurs. I think the problem is in connecting *phenoData* to *annotation*, but I'm not sure how to do this. I would like to connect the *exprs* to * annotation*, to connect Chip and Block numbers, but I don't see how to do this. Any help would be greatly appreciated! > sponge_ExpressionSet<-new("ExpressionSet",exprs=sponge_data,phenoDat a=samples_matrix,experimentData=experimentData,annotation=annotation_m atrix)Error: ExpressionSet 'phenoData' is class 'matrix' but should be or extend 'AnnotatedDataFrame' Thank you! Lisa [[alternative HTML version deleted]]

Dear Lisa, > I'm using the Biobase package to build an ExpressionSet from scratch using > data from a custom 8x15k Agilent microarray. I'm getting this error and > can't quite figure it out. Does anyone know how *phenoData* can extend the * > annotation*? I would like to connect *phenoData* to *exprs* with the Chip > and Block numbers, somehow, but I don't know how to do this. Any help would > be greatly appreciated! > >> sponge_ExpressionSet<-new("ExpressionSet",exprs=sponge_data,phenoDa ta=samples_matrix,experimentData=experimentData,annotation=annotation_ matrix)Error: ExpressionSet 'phenoData' is class 'matrix' but should be or extend 'AnnotatedDataFrame' The message tells you that the content of the phenoData slot must be an 'AnnotateDataFrame'. Once you have it as a data.frame, you can do the following pd <- new("AnnotatedDataFrame", data = pddataframe) and then pass phenoData = pd in the constructor. This also holds for the featureData slot. The expression data, on the other hand must be a matrix (not a data.frame). Hope this helps. Best wishes, Laurent > > Details: > > These are the instructions that I am following: > http://www.bioconductor.org/help/course- materials/2006/biocintro_oct/labs/ExpressionSet/ExpressionSetIntro- lab.pdf > http://www.bioconductor.org/packages/2.13/bioc/vignettes/Biobase/ins t/doc/ExpressionSetIntroduction.pdf > > 1. *exprs* data (sponge_data) were extracted from GenePix *.gpr files and > are in a 15744 x 72 double matrix with RefNumber as rownames: > >> head(sponge_data) > > Block 1 Chip 1 Block 2 Chip 1 Block 3 Chip 1 Block 4 Chip 1 Block 5 Chip 1 > 15744 2 23 6 9 3 > 15580 9 16 11 11 6 > 15416 1 0 0 0 1 > 15252 1 0 0 -1 0 > 15088 3 2 0 1 0 > 14924 0 -1 0 0 1 > > > 2. *phenoData* (samples_matrix) is a 72 x 8 character matrix with > experimental design variables for each chip and block: > >> head(samples_matrix) Chip Number File Name Hyb Date Tank Treatment Colony Raceway > [1,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "C3" "UC" > "P" "B" > [2,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "B2" "UD" > "P" "A" > [3,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "B2" "UD" > "O" "A" > [4,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "D3" "OD" > "BL" "A" > [5,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "D1" "OD" > "O" "B" > [6,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "C3" "UC" > "O" "B" > >> all(rownames(samples_matrix)==colnames(sponge_data))[1] TRUE > > > 3. *annotation* is (annotation_matrix) is a 15744 x 23 character matrix > with microarray annotation info, including RefNumber: > >> head(annotation_matrix) Column Row RefNumber Name Append Name > [1,] "96" "164" " 1" "GE_BrightCorner" "GE_BrightCorner" > [2,] "96" "162" " 2" "DarkCorner" "DarkCorner" > [3,] "96" "160" " 3" "DarkCorner" "DarkCorner" > [4,] "96" "158" " 4" "222803147_EZ031535.1" > "222803147_EZ031535.1_16-465" > [5,] "96" "156" " 5" "222546129_EZ002319.1" > "222546129_EZ002319.1_1845-2030" > [6,] "96" "154" " 6" "222801996_EZ030384.1" > "222801996_EZ030384.1_31-2558" > >> all(rownames(annotation_matrix)==rownames(sponge_data))[1] TRUE > > > 4. experimentData (experimentData): metadata info > > But, when I go to finally assemble the ExpressionSet, the error below > occurs. I think the problem is in connecting *phenoData* to *annotation*, > but I'm not sure how to do this. I would like to connect the *exprs* to * > annotation*, to connect Chip and Block numbers, but I don't see how to do > this. Any help would be greatly appreciated! > >> sponge_ExpressionSet<-new("ExpressionSet",exprs=sponge_data,phenoDa ta=samples_matrix,experimentData=experimentData,annotation=annotation_ matrix)Error: ExpressionSet 'phenoData' is class 'matrix' but should be or extend 'AnnotatedDataFrame' > > > > Thank you! > Lisa > > [[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

lisa.johnson.cohen at gmail.com writes: > Hi Laurent, Thank you for your message. It helped tremendously. I converted > my data to a matrix and also had to fiddle around a bit get the row and > column names to match up. But, I successfully made the ExpressionSet! Thank > you so much. Great! > sponge_ExpressionSet<-new("ExpressionSet",exprs=sponge_data,phenoDat a=pd,experimentData=experimentData,featureData=an) > > Do you by any chance work with custom microarrays? We use custom Agilent > microarrays. Do you have any suggetions for quality assessment? The best place to look for microarray quality is probably the arrayQualityMetrics package [1]. I have never tried it with an ExpressionSet built from a custom Agilent array though. Best wishes, Laurent [1] http://www.bioconductor.org/packages/release/bioc/html/arrayQualit yMetrics.html > Thank you again! > Lisa > > --- > Lisa Cohen, M.Sc. > Marine Ecosystem Health, > Harbor Branch Oceanographic Institute > at Florida Atlantic University > 5600 N. US Hwy 1 > Fort Pierce, FL 34946 > Phone: (772) 242-2396 > Fax: (772) 468-0757 > Email:lcohen49 at hboi.fau.edu > Alt. Email: lisa.johnson.cohen at gmail.com > > <lcohen49 at="" hboi.fau.edu=""> > > > > > > On Wed, Oct 16, 2013 at 4:44 PM, Laurent Gatto <lg390 at="" cam.ac.uk=""> wrote: > >> >> Dear Lisa, >> >> > I'm using the Biobase package to build an ExpressionSet from scratch >> using >> > data from a custom 8x15k Agilent microarray. I'm getting this error and >> > can't quite figure it out. Does anyone know how *phenoData* can extend >> the * >> > annotation*? I would like to connect *phenoData* to *exprs* with the Chip >> > and Block numbers, somehow, but I don't know how to do this. Any help >> would >> > be greatly appreciated! >> > >> >> >> sponge_ExpressionSet<-new("ExpressionSet",exprs=sponge_data,phenoDa ta=samples_matrix,experimentData=experimentData,annotation=annotation_ matrix)Error: >> ExpressionSet 'phenoData' is class 'matrix' but should be or extend >> 'AnnotatedDataFrame' >> >> The message tells you that the content of the phenoData slot must be an >> 'AnnotateDataFrame'. Once you have it as a data.frame, you can do the >> following >> >> pd <- new("AnnotatedDataFrame", data = pddataframe) >> >> and then pass phenoData = pd in the constructor. >> >> This also holds for the featureData slot. >> >> The expression data, on the other hand must be a matrix (not a >> data.frame). >> >> Hope this helps. >> >> Best wishes, >> >> Laurent >> >> > >> > Details: >> > >> > These are the instructions that I am following: >> > >> http://www.bioconductor.org/help/course- materials/2006/biocintro_oct/labs/ExpressionSet/ExpressionSetIntro- lab.pdf >> > >> http://www.bioconductor.org/packages/2.13/bioc/vignettes/Biobase/in st/doc/ExpressionSetIntroduction.pdf >> > >> > 1. *exprs* data (sponge_data) were extracted from GenePix *.gpr files and >> > are in a 15744 x 72 double matrix with RefNumber as rownames: >> > >> >> head(sponge_data) >> > >> > Block 1 Chip 1 Block 2 Chip 1 Block 3 Chip 1 Block 4 Chip 1 Block >> 5 Chip 1 >> > 15744 2 23 6 9 >> 3 >> > 15580 9 16 11 11 >> 6 >> > 15416 1 0 0 0 >> 1 >> > 15252 1 0 0 -1 >> 0 >> > 15088 3 2 0 1 >> 0 >> > 14924 0 -1 0 0 >> 1 >> > >> > >> > 2. *phenoData* (samples_matrix) is a 72 x 8 character matrix with >> > experimental design variables for each chip and block: >> > >> >> head(samples_matrix) Chip Number File Name Hyb >> Date Tank Treatment Colony Raceway >> > [1,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "C3" "UC" >> > "P" "B" >> > [2,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "B2" "UD" >> > "P" "A" >> > [3,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "B2" "UD" >> > "O" "A" >> > [4,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "D3" "OD" >> > "BL" "A" >> > [5,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "D1" "OD" >> > "O" "B" >> > [6,] "1" "253295110067_2012-08-01.txt" "8/1/2012" "C3" "UC" >> > "O" "B" >> > >> >> all(rownames(samples_matrix)==colnames(sponge_data))[1] TRUE >> > >> > >> > 3. *annotation* is (annotation_matrix) is a 15744 x 23 character matrix >> > with microarray annotation info, including RefNumber: >> > >> >> head(annotation_matrix) Column Row RefNumber Name Append >> Name >> > [1,] "96" "164" " 1" "GE_BrightCorner" "GE_BrightCorner" >> > [2,] "96" "162" " 2" "DarkCorner" "DarkCorner" >> > [3,] "96" "160" " 3" "DarkCorner" "DarkCorner" >> > [4,] "96" "158" " 4" "222803147_EZ031535.1" >> > "222803147_EZ031535.1_16-465" >> > [5,] "96" "156" " 5" "222546129_EZ002319.1" >> > "222546129_EZ002319.1_1845-2030" >> > [6,] "96" "154" " 6" "222801996_EZ030384.1" >> > "222801996_EZ030384.1_31-2558" >> > >> >> all(rownames(annotation_matrix)==rownames(sponge_data))[1] TRUE >> > >> > >> > 4. experimentData (experimentData): metadata info >> > >> > But, when I go to finally assemble the ExpressionSet, the error below >> > occurs. I think the problem is in connecting *phenoData* to *annotation*, >> > but I'm not sure how to do this. I would like to connect the *exprs* to * >> > annotation*, to connect Chip and Block numbers, but I don't see how to do >> > this. Any help would be greatly appreciated! >> > >> >> >> sponge_ExpressionSet<-new("ExpressionSet",exprs=sponge_data,phenoDa ta=samples_matrix,experimentData=experimentData,annotation=annotation_ matrix)Error: >> ExpressionSet 'phenoData' is class 'matrix' but should be or extend >> 'AnnotatedDataFrame' >> > >> > >> > >> > Thank you! >> > Lisa >> > >> > [[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 >> >>