[BioC] annotating lumi
Gilbert Feng
g-feng at northwestern.edu
Fri May 21 17:59:26 CEST 2010
Hi, Katie
Just reminder, in the following scripts, you type filename, not fileName in
lumiR function.
>> fileName <- 'raw_data_lumi_21.txt'
>> katie.lumi = lumiR(filename, sampleInfoFile='sample_table_21.txt',
>> convertNuID=FALSE)
> Error in file.exists(fileName) : object 'filename' not found
One easy way is to follow the instruction in lumi vignette and you can use
lookUp function to map nuIDs to any other IDs in lumiHumanAll.db .
Gilbert
On 5/21/10 6:43 AM, "Taylor, Katie" <kt70 at leicester.ac.uk> wrote:
> Hi,
>
> I am trying to annotate my illumina microarray using the following script that
> I found online. However, I am having some difficulties with it as it is not
> writing out the annotation data with the normalised data. Also, using this
> script means that I don't know how to load in the sample file info. I have
> copied the script that I used and the R output and session info below. Any
> help would be greatly appreciated.
>
>
> Script:
>
>> library(lumi)
>> fileName <- 'raw_data_lumi_21.txt'
>> katie.lumi = lumiR(fileName, convertNuID=FALSE)
>> katie.lumi = addNuID2lumi(katie.lumi,
> + annotationFile='HUMANREF-8_V3_0_R1_11282963_A_WGDASL',
> + annotationColName=c(sequence='Probe_Sequence', probe='Probe_Id',
> symbol='Symbol'))
>> katie.lumi
>> summary(katie.lumi, 'QC')
>> lumi.T <- lumiT(katie.lumi)
>> lumi.N <- lumiN(lumi.T)
>> lumi.N.Q <- lumiQ(lumi.N)
>> summary(lumi.N.Q, 'QC')
>> write.exprs(lumi.N.Q, file='normkatieData21anno.txt')
>
>
> R output:
>
>> library(lumi)
> Loading required package: annotate
> Loading required package: AnnotationDbi
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
> Vignettes contain introductory material. To view, type
> 'openVignette()'. To cite Bioconductor, see
> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: affy
> Loading required package: mgcv
> This is mgcv 1.6-1. For overview type `help("mgcv-package")'.
> Loading required package: preprocessCore
> Loading required package: RSQLite
> Loading required package: DBI
> Loading required package: MASS
>> fileName <- 'raw_data_lumi_21.txt'
>> katie.lumi = lumiR(filename, sampleInfoFile='sample_table_21.txt',
>> convertNuID=FALSE)
> Error in file.exists(fileName) : object 'filename' not found
>> katie.lumi = lumiR(fileName, sampleInfoFile='sample_table_21.txt',
>> convertNuID=FALSE)
> Error in read.table(file = fileName, header = TRUE, sep = sep, dec = dec, :
> unused argument(s) (sampleInfoFile = "sample_table_21.txt")
>> katie.lumi = lumiR(fileName, convertNuID=FALSE)
> Perform Quality Control assessment of the LumiBatch object ...
>> katie.lumi = addNuID2lumi(katie.lumi,
> + annotationFile='HUMANREF-8_V3_0_R1_11282963_A_WGDASL',
> + annotationColName=c(sequence='Probe_Sequence', probe='Probe_Id',
> symbol='Symbol'))
> Directly converting probe sequence to nuIDs ...
>> katie.lumi
> Summary of data information:
> Data File Information:
>
>
> Major Operation History:
> submitted finished
> 1 2010-05-21 12:28:46 2010-05-21 12:29:12
> 2 2010-05-21 12:29:12 2010-05-21 12:29:13
> 3 2010-05-21 12:30:14 2010-05-21 12:30:19
> 4 2010-05-21 12:30:14 2010-05-21 12:30:19
> 5 2010-05-21 12:30:14 2010-05-21 12:30:19
>
> command
> 1 lumiR("raw_data_lumi_21.txt",
> convertNuID = FALSE)
> 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh,
> verbose = verbose)
> 3 addNuID2lumi(x.lumi = katie.lumi, annotationFile =
> "HUMANREF-8_V3_0_R1_11282963_A_WGDASL",
> 4 annotationColName = c(sequence = "Probe_Sequence", probe
> = "Probe_Id",
> 5
> symbol = "Symbol"))
> lumiVersion
> 1 1.14.0
> 2 1.14.0
> 3 1.14.0
> 4 1.14.0
> 5 1.14.0
>
> Object Information:
> LumiBatch (storageMode: lockedEnvironment)
> assayData: 24526 features, 21 samples
> element names: detection, exprs, se.exprs
> protocolData: none
> phenoData
> sampleNames: NC37, NC54, ..., KT27P (21 total)
> varLabels and varMetadata description:
> sampleID: The unique Illumina microarray Id
> featureData
> featureNames: Ku8QhfS0n_hIOABXuE, fqPEquJRRlSVSfL.8A, ...,
> N8t5EuJCr0Tk9.zHno (24526 total)
> fvarLabels and fvarMetadata description:
> ProbeID: The Illumina microarray identifier
> TargetID: The Illumina TargetID
> ...: ...
> PROBE_COORDINATES: PROBE_COORDINATES
> (8 total)
> experimentData: use 'experimentData(object)'
> Annotation: lumiHumanAll.db
> Control Data: Available
> QC information: Please run summary(x, 'QC') for details!
>> summary(katie.lumi, 'QC')
> Data dimension: 24526 genes x 21 samples
>
> Summary of Samples:
> NC37 NC54 NC2 NC5 HP13 HP3
> mean 8.8950 7.8930 8.8250 9.0190 9.3190 9.6140
> standard deviation 2.5030 2.7780 2.5320 2.6240 2.2480 2.4370
> detection rate(0.01) 0.7478 0.5166 0.7178 0.7182 0.8265 0.8145
> distance to sample mean 284.1000 335.4000 266.7000 298.7000 212.2000 282.8000
> HP27 HP75 A190N A4N A190P A4P
> mean 8.5520 8.1660 8.4600 8.1760 8.0330 8.5530
> standard deviation 2.5050 2.4220 2.7490 2.9450 2.4510 2.9110
> detection rate(0.01) 0.6902 0.6741 0.5803 0.4607 0.6253 0.5407
> distance to sample mean 243.8000 252.8000 299.3000 352.6000 263.0000 353.8000
> A10P KT65N KT50N KT01N KT27N KT65P
> mean 9.7460 9.4720 8.5610 9.3940 8.4880 8.1720
> standard deviation 2.4930 2.6780 2.7550 2.2790 2.7980 2.8650
> detection rate(0.01) 0.7805 0.7237 0.6034 0.8054 0.5725 0.5004
> distance to sample mean 338.7000 338.3000 317.2000 233.3000 316.2000 350.8000
> KT50P KT01P KT27P
> mean 8.5120 8.1190 8.6020
> standard deviation 2.7240 2.4180 2.4280
> detection rate(0.01) 0.5722 0.6046 0.6863
> distance to sample mean 305.1000 246.4000 232.5000
>
> Major Operation History:
> submitted finished
> 1 2010-05-21 12:28:46 2010-05-21 12:29:12
> 2 2010-05-21 12:29:12 2010-05-21 12:29:13
> command
> 1 lumiR("raw_data_lumi_21.txt", convertNuID = FALSE)
> 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose)
> lumiVersion
> 1 1.14.0
> 2 1.14.0
>> lumi.T <- lumiT(katie.lumi)
> Perform vst transformation ...
> No Standard Deviation correction was applied becasue of missing bead number
> information.
> 2010-05-21 12:31:05 , processing array 1
> 2010-05-21 12:31:06 , processing array 2
> 2010-05-21 12:31:06 , processing array 3
> 2010-05-21 12:31:06 , processing array 4
> 2010-05-21 12:31:06 , processing array 5
> 2010-05-21 12:31:06 , processing array 6
> 2010-05-21 12:31:06 , processing array 7
> 2010-05-21 12:31:06 , processing array 8
> 2010-05-21 12:31:06 , processing array 9
> 2010-05-21 12:31:06 , processing array 10
> 2010-05-21 12:31:07 , processing array 11
> 2010-05-21 12:31:07 , processing array 12
> 2010-05-21 12:31:07 , processing array 13
> 2010-05-21 12:31:07 , processing array 14
> 2010-05-21 12:31:07 , processing array 15
> 2010-05-21 12:31:07 , processing array 16
> 2010-05-21 12:31:07 , processing array 17
> 2010-05-21 12:31:08 , processing array 18
> 2010-05-21 12:31:08 , processing array 19
> 2010-05-21 12:31:08 , processing array 20
> 2010-05-21 12:31:08 , processing array 21
>> lumi.N <- lumiN(lumi.T)
> Perform quantile normalization ...
>> lumi.N.Q <- lumiQ(lumi.N)
> Perform Quality Control assessment of the LumiBatch object ...
>> summary(lumi.N.Q, 'QC')
> Data dimension: 24526 genes x 21 samples
>
> Summary of Samples:
> NC37 NC54 NC2 NC5 HP13 HP3
> mean 9.1660 9.1660 9.1660 9.1660 9.1660 9.1660
> standard deviation 1.9660 1.9660 1.9660 1.9660 1.9660 1.9660
> detection rate(0.01) 0.7478 0.5166 0.7178 0.7182 0.8265 0.8145
> distance to sample mean 204.5000 221.7000 186.4000 198.6000 153.3000 168.0000
> HP27 HP75 A190N A4N A190P A4P
> mean 9.1660 9.1660 9.1660 9.1660 9.1660 9.1660
> standard deviation 1.9660 1.9660 1.9660 1.9660 1.9660 1.9660
> detection rate(0.01) 0.6902 0.6741 0.5803 0.4607 0.6253 0.5407
> distance to sample mean 181.1000 192.1000 203.0000 232.5000 190.6000 233.2000
> A10P KT65N KT50N KT01N KT27N KT65P
> mean 9.1660 9.1660 9.1660 9.1660 9.1660 9.1660
> standard deviation 1.9660 1.9660 1.9660 1.9660 1.9660 1.9660
> detection rate(0.01) 0.7805 0.7237 0.6034 0.8054 0.5725 0.5004
> distance to sample mean 215.5000 218.1000 216.5000 163.1000 214.3000 236.7000
> KT50P KT01P KT27P
> mean 9.1660 9.1660 9.1660
> standard deviation 1.9660 1.9660 1.9660
> detection rate(0.01) 0.5722 0.6046 0.6863
> distance to sample mean 211.7000 186.3000 175.6000
>
> Major Operation History:
> submitted finished
> 1 2010-05-21 12:28:46 2010-05-21 12:29:12
> 2 2010-05-21 12:29:12 2010-05-21 12:29:13
> 3 2010-05-21 12:30:14 2010-05-21 12:30:19
> 4 2010-05-21 12:30:14 2010-05-21 12:30:19
> 5 2010-05-21 12:30:14 2010-05-21 12:30:19
> 6 2010-05-21 12:31:04 2010-05-21 12:31:08
> 7 2010-05-21 12:31:19 2010-05-21 12:31:19
> 8 2010-05-21 12:31:28 2010-05-21 12:31:28
>
> command
> 1 lumiR("raw_data_lumi_21.txt",
> convertNuID = FALSE)
> 2 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh,
> verbose = verbose)
> 3 addNuID2lumi(x.lumi = katie.lumi, annotationFile =
> "HUMANREF-8_V3_0_R1_11282963_A_WGDASL",
> 4 annotationColName = c(sequence = "Probe_Sequence", probe
> = "Probe_Id",
> 5
> symbol = "Symbol"))
> 6
> lumiT(x.lumi = katie.lumi)
> 7
> lumiN(x.lumi = lumi.T)
> 8
> lumiQ(x.lumi = lumi.N)
> lumiVersion
> 1 1.14.0
> 2 1.14.0
> 3 1.14.0
> 4 1.14.0
> 5 1.14.0
> 6 1.14.0
> 7 1.14.0
> 8 1.14.0
>> write.exprs(lumi.N.Q, file='normkatieData21anno.txt')
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] lumi_1.14.0 MASS_7.3-5 RSQLite_0.8-4
> [4] DBI_0.2-5 preprocessCore_1.10.0 mgcv_1.6-1
> [7] affy_1.26.0 annotate_1.26.0 AnnotationDbi_1.10.0
> [10] Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0 grid_2.11.0 lattice_0.18-5
> Matrix_0.999375-38
> [5] nlme_3.1-96 tools_2.11.0 xtable_1.5-6
>>
>
>
> I hope someone can help me with this. Thank you in advance.
>
> Katie
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