[BioC] Illumina data and GO2heatmap
Lavinia Gordon
lavinia.gordon at mcri.edu.au
Fri Jun 18 05:26:54 CEST 2010
Hi Mervi,
I think the error is because your test object does not contain any
probes that are within the KEGG pathway '04810', the object is too small.
Try exactly the same command but use your entire lumi batch object
rather than a subset (test) and see if that works.
cheers
Lavinia.
> Message: 15
> Date: Wed, 16 Jun 2010 12:36:40 +0000
> From: "Alanne, Mervi"<Mervi.Alanne at wri.fi>
> To: Marc Carlson<mcarlson at fhcrc.org>
> Cc: "bioconductor at stat.math.ethz.ch"<bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Illumina data and GO2heatmap
> Message-ID:
> <09A552FBFB71DD4EBEABA1F9F4A7BFAE017ECD at WRISRV.wri-tl.local>
> Content-Type: text/plain
>
> 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 at fhcrc.org]
> Sent: 14. kesäkuuta 2010 19:39
> To: bioconductor at 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
>
>
>
>
>
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--
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