[BioC] annotating lumi
Taylor, Katie
kt70 at leicester.ac.uk
Fri May 21 13:43:43 CEST 2010
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
More information about the Bioconductor
mailing list