Hi Mervi,

So I still can't reproduce this exactly since your attachments are
blocked, if you really need to me to reproduce it, please send me the
attachment to my personal email instead.  But even without that I think
I know what the problem is.  When you pass in a GO term here you have to
leave on the "GO:" prefix.  So I think that this command will work for you:

GO2heatmap("GO:0002697", test, "lumiHumanAll")

Again, I don't have your data, so I can't be 100% certain.  If for
example none of the probes in test were associated with GO:0002697, then
it would also be impossible for heatmap to do it's job.  But assuming
that this is not the case, then it should work if you prepend "GO:" onto
your GO term.


  Marc





On 06/16/2010 05:36 AM, Alanne, Mervi wrote:
>
> Hi Marc,
>
>  
>
> Thank you for your reply. For some reason I didn't receive your first
> reply and thought that my question was still waiting for moderator
> approval.
>
>  
>
> Your tip helped a bit, but the function doesn't still work. Maybe it
> is because lumi batch object is a S4 class object? I'm not familiar
> with Affy eSet objects and can't compare them to lumi objects. (I
> atteched the structure of the lumi batch object) If you or someone can
> help, I would greatly appreciate it.
>
>  
>
> -Mervi
>
>  
>
>  
>
>  
>
> library("lumiHumanAll.db")
>
> library("lumi")
>
> library("annotate")
>
> test <-lumi22.Q[immune_nu]
>
> str(test)
>
> Formal class 'LumiBatch' [package "lumi"] with 10 slots
>
>   ..@ history          :'data.frame':   7 obs. of  4 variables:
>
>   .. ..$ submitted  : chr [1:7] "2010-05-18 11:28:36" "2010-05-18
> 11:28:36" "2010-05-18 11:29:34" "2010-05-18 11:29:55" ...
>
>   .. ..$ finished   : chr [1:7] "2010-05-18 11:29:33" "2010-05-18
> 11:29:33" "2010-05-18 11:29:36" "2010-05-18 11:29:56" ...
>
>   .. ..$ command    : chr [1:7]
> "lumiR(\"P:/wri_illu/data/data_22.txt\", " "    QC = TRUE)"
> "lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose)"
> "Subsetting 48803 features." ...
>
>   .. ..$ lumiVersion: chr [1:7] "1.12.4" "1.12.4" "1.12.4" "1.12.4" ...
>
>   ..@ controlData      :'data.frame':   0 obs. of  0 variables
>
>   ..@ QC               :List of 3
>
>   .. ..$ BeadStudioSummary:'data.frame':        0 obs. of  0 variables
>
>   .. ..$ sampleSummary    : num [1:4, 1:22] 7.206 1.299 0.317 47.19
> 7.278 ...
>
>   .. .. ..- attr(*, "dimnames")=List of 2
>
>   .. .. .. ..$ : chr [1:4] "mean" "standard deviation" "detection
> rate(0.05)" "distance to sample mean"
>
>   .. .. .. ..$ : chr [1:22] "X5050496005_A" "X5050496005_B"
> "X5050496005_C" "X5050496005_D" ...
>
>   .. ..$ history          :'data.frame':        6 obs. of  4 variables:
>
>   .. .. ..$ submitted  : chr [1:6] "2010-05-18 11:28:36" "2010-05-18
> 11:28:36" "2010-05-18 11:29:34" "2010-05-18 11:29:55" ...
>
>   .. .. ..$ finished   : chr [1:6] "2010-05-18 11:29:33" "2010-05-18
> 11:29:33" "2010-05-18 11:29:36" "2010-05-18 11:29:56" ...
>
>   .. .. ..$ command    : chr [1:6]
> "lumiR(\"P:/wri_illu/data/data_22.txt\", " "    QC = TRUE)"
> "lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose)"
> "Subsetting 48803 features." ...
>
>   .. .. ..$ lumiVersion: chr [1:6] "1.12.4" "1.12.4" "1.12.4" "1.12.4" ...
>
>   ..@ assayData        :<environment: 0x11619e3c>
>
>   ..@ phenoData        :Formal class 'AnnotatedDataFrame' [package
> "Biobase"] with 4 slots
>
>   .. .. ..@ varMetadata      :'data.frame':     1 obs. of  1 variable:
>
>   .. .. .. ..$ labelDescription: chr "The unique Illumina microarray Id"
>
>   .. .. ..@ data             :'data.frame':     22 obs. of  1 variable:
>
>   .. .. .. ..$ sampleID: chr [1:22] "X5050496005_A" "X5050496005_B"
> "X5050496005_C" "X5050496005_D" ...
>
>   .. .. ..@ dimLabels        : chr [1:2] "sampleNames" "sampleColumns"
>
>   .. .. ..@ .__classVersion__:Formal class 'Versions' [package
> "Biobase"] with 1 slots
>
>   .. .. .. .. ..@ .Data:List of 1
>
>   .. .. .. .. .. ..$ : int [1:3] 1 1 0
>
>   ..@ featureData      :Formal class 'AnnotatedDataFrame' [package
> "Biobase"] with 4 slots
>
>   .. .. ..@ varMetadata      :'data.frame':     8 obs. of  1 variable:
>
>   .. .. .. ..$ labelDescription: chr [1:8] "The Illumina microarray
> identifier" "The Illumina TargetID" "ACCESSION" "SYMBOL" ...
>
>   .. .. ..@ data             :'data.frame':     22 obs. of  8 variables:
>
>   .. .. .. ..$ ProbeID              : chr [1:22] "2030309" "1090747"
> "2650156" "4830255" ...
>
>   .. .. .. ..$ TargetID             : chr [1:22] "SERPING1" "TNFSF12"
> "TAP2" "DPP4" ...
>
>   .. .. .. ..$ ACCESSION            : chr [1:22] "NM_001032295.1"
> "NM_003809.2" "NM_018833.2" "NM_001935.3" ...
>
>   .. .. .. ..$ SYMBOL               : chr [1:22] "SERPING1" "TNFSF12"
> "TAP2" "DPP4" ...
>
>   .. .. .. ..$ PROBE_START          : int [1:22] 1483 1146 1448 3620
> 1940 1981 3561 244 1453 1365 ...
>
>   .. .. .. ..$ CHROMOSOME           : chr [1:22] "11" "17" "6" "2" ...
>
>   .. .. .. ..$ PROBE_CHR_ORIENTATION: chr [1:22] "+" "+" "-" "-" ...
>
>   .. .. .. ..$ PROBE_COORDINATES    : chr [1:22] "53730786-53730835"
> "7401691-7401740" "32906458-32906507" "154730867-154730916" ...
>
>   .. .. ..@ dimLabels        : chr [1:2] "featureNames" "featureColumns"
>
>   .. .. ..@ .__classVersion__:Formal class 'Versions' [package
> "Biobase"] with 1 slots
>
>   .. .. .. .. ..@ .Data:List of 1
>
>   .. .. .. .. .. ..$ : int [1:3] 1 1 0
>
>   ..@ experimentData   :Formal class 'MIAME' [package "Biobase"] with
> 13 slots
>
>   .. .. ..@ name             : chr ""
>
>   .. .. ..@ lab              : chr ""
>
>   .. .. ..@ contact          : chr ""
>
>   .. .. ..@ title            : chr ""
>
>   .. .. ..@ abstract         : chr ""
>
>   .. .. ..@ url              : chr ""
>
>   .. .. ..@ pubMedIds        : chr ""
>
>   .. .. ..@ samples          : list()
>
>   .. .. ..@ hybridizations   : list()
>
>   .. .. ..@ normControls     : list()
>
>   .. .. ..@ preprocessing    : list()
>
>   .. .. ..@ other            :List of 1
>
>   .. .. .. ..$ Data File Information: NULL
>
>   .. .. ..@ .__classVersion__:Formal class 'Versions' [package
> "Biobase"] with 1 slots
>
>   .. .. .. .. ..@ .Data:List of 1
>
>   .. .. .. .. .. ..$ : int [1:3] 1 0 0
>
>   ..@ annotation       : chr "lumiHumanAll.db"
>
>   ..@ protocolData     :Formal class 'AnnotatedDataFrame' [package
> "Biobase"] with 4 slots
>
>   .. .. ..@ varMetadata      :'data.frame':     0 obs. of  1 variable:
>
>   .. .. .. ..$ labelDescription: chr(0)
>
>   .. .. ..@ data             :'data.frame':     22 obs. of  0 variables
>
>   .. .. ..@ dimLabels        : chr [1:2] "sampleNames" "sampleColumns"
>
>   .. .. ..@ .__classVersion__:Formal class 'Versions' [package
> "Biobase"] with 1 slots
>
>   .. .. .. .. ..@ .Data:List of 1
>
>   .. .. .. .. .. ..$ : int [1:3] 1 1 0
>
>   ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"]
> with 1 slots
>
>   .. .. ..@ .Data:List of 4
>
>   .. .. .. ..$ : int [1:3] 2 10 1
>
>   .. .. .. ..$ : int [1:3] 2 6 1
>
>   .. .. .. ..$ : int [1:3] 1 3 0
>
>   .. .. .. ..$ : int [1:3] 1 0 0
>
> > GO2heatmap("0002697", test, "lumiHumanAll")
>
> Error in heatmap(dataM, ...) :
>
>   'x' must have at least 2 rows and 2 columns
>
>  
>
>  
>
> R version 2.10.1 (2009-12-14)
>
> i386-pc-mingw32
>
>  
>
> locale:
>
> [1] LC_COLLATE=Finnish_Finland.1252  LC_CTYPE=Finnish_Finland.1252  
>
> [3] LC_MONETARY=Finnish_Finland.1252 LC_NUMERIC=C                    
>
> [5] LC_TIME=Finnish_Finland.1252   
>
>  
>
> attached base packages:
>
> [1] grDevices datasets  splines   graphics  stats     tcltk    
> utils     methods   base    
>
>  
>
> other attached packages:
>
> [1] lumi_1.12.4           MASS_7.3-5            preprocessCore_1.8.0 
> mgcv_1.6-2          
>
>  [5] affy_1.24.2           annotate_1.24.1       lumiHumanAll.db_1.8.1
> org.Hs.eg.db_2.3.6  
>
>  [9] RSQLite_0.8-2         DBI_0.2-5             AnnotationDbi_1.8.1  
> Biobase_2.6.1       
>
> [13] svSocket_0.9-48       TinnR_1.0.3           R2HTML_2.1           
> Hmisc_3.8-1         
>
> [17] survival_2.35-8     
>
>  
>
> loaded via a namespace (and not attached):
>
> [1] affyio_1.14.0      cluster_1.12.3     grid_2.10.1       
> lattice_0.18-3   
>
> [5] Matrix_0.999375-40 nlme_3.1-96        svMisc_0.9-57     
> tools_2.10.1     
>
> [9] xtable_1.5-6 
>
>  
>
>  
>
>  
>
> *From:* Marc Carlson [mailto:mcarlson@fhcrc.org]
> *Sent:* 14. kesäkuuta 2010 19:39
> *To:* bioconductor@stat.math.ethz.ch; Alanne, Mervi
> *Subject:* Re: [BioC] Illumina data and GO2heatmap
>
>  
>
> Hi Mervi. 
>
> As I stated before, I believe this should work.  You will have to plot
> it like this though because the chip type does not have a ".db"
> extension.  Only the annotation package has that.
>
> library("lumiHumanAll.db")
> KEGG2heatmap("04810", test, "lumiHumanAll")
>
> If you try this and it doesn't work just let us know.
>
>
>   Marc
>
>
>
> On 06/14/2010 05:45 AM, Alanne, Mervi wrote:
>
> Dear all,
>  
> Is it possible to plot expression data from Illumina HT-12 with GO2heatmap or KEGG2heatmap functions? I'm using lumi package for normalizing and transforming the data and I understand that the lumi batch objects have the same structure as eSet. However when I try to use the function on lumi object with lumiHumanAll.db annotation I get error messages saying that " object 'lumiHumanAll.dbPATH2PROBE' not found". Apperantly PATH2PROBE is missing from the lumi object ?
>  
>   
>
>     library("lumiHumanAll.db")
>
>     KEGG2heatmap("04810", test, "lumiHumanAll.db")
>
>         
>
>  
> -Mervi
> Dr. Mervi Kinnunen (née Alanne)
> Postdoctoral fellow
> Wihuri Research Institute
> Finland
>  
>  
>     [[alternative HTML version deleted]]
>  
>   
>  
>  
> _______________________________________________
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>
>  
>


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