[BioC] help with lumi
Taylor, Katie
kt70 at leicester.ac.uk
Thu May 20 15:25:09 CEST 2010
Hi,
I have just tried to load illumina microarray data into lumi and I added loadAnnotaion=TRUE. However, when I output the data to an .txt document, only the nuIDs are there and the annotation has gone. Does anyone know what i've done wrong?
Also, I have 24 samples, with 6 groups. How do I perform comparisons between the groups using limma? Can I do all of the comparisons at once, producing different documents for each or is it better to do each comparison individually? I would appreciate your comments.
I have copied the session info and R output for lumi below:
R version 2.11.0 (2010-04-22)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
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'citation()' on how to cite R or R packages in publications.
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> 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.batch(fileName, sampleInfoFile='sample_table_21.txt', inputAnnotation = TRUE)
Inputting the data ...
Adding nuID to the data ...
Directly converting probe sequence to nuIDs ...
Perform Quality Control assessment of the LumiBatch object ...
> katie.lumi
Summary of data information:
Data File Information:
Major Operation History:
submitted finished
1 2010-05-20 14:00:37 2010-05-20 14:01:08
2 2010-05-20 14:00:37 2010-05-20 14:01:08
3 2010-05-20 14:01:08 2010-05-20 14:01:08
command
1 lumiR.batch("raw_data_lumi_21.txt",
2 inputAnnotation = TRUE)
3 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose)
lumiVersion
1 1.14.0
2 1.14.0
3 1.14.0
Object Information:
LumiBatch (storageMode: lockedEnvironment)
assayData: 24526 features, 21 samples
element names: detection, exprs, se.exprs
protocolData: none
phenoData
rowNames: NC37, NC54, ..., KT27P (21 total)
varLabels and varMetadata description:
Index: NA
sampleID: NA
...: ...
Noise: NA
(22 total)
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 2010-05-20 14:00:37 2010-05-20 14:01:08
2 2010-05-20 14:00:37 2010-05-20 14:01:08
3 2010-05-20 14:01:08 2010-05-20 14:01:08
command
1 lumiR.batch("raw_data_lumi_21.txt",
2 inputAnnotation = TRUE)
3 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose)
lumiVersion
1 1.14.0
2 1.14.0
3 1.14.0
> pdf("plots.pdf")
> plot(katie.lumi, what='density')
> density(katie.lumi)
> plotCDF(katie.lumi, reverse=TRUE)
> plot(katie.lumi, what='pair')
> pairs(katie.lumi, smoothScatter=T)
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
> MAplot(katie.lumi, smoothScatter=TRUE)
> plot(katie.lumi, what='cv')
> plot(katie.lumi, what='boxplot')
> lumi.T <- lumiT(katie.lumi)
Perform vst transformation ...
No Standard Deviation correction was applied becasue of missing bead number information.
2010-05-20 14:16:47 , processing array 1
2010-05-20 14:16:47 , processing array 2
2010-05-20 14:16:47 , processing array 3
2010-05-20 14:16:47 , processing array 4
2010-05-20 14:16:47 , processing array 5
2010-05-20 14:16:47 , processing array 6
2010-05-20 14:16:47 , processing array 7
2010-05-20 14:16:47 , processing array 8
2010-05-20 14:16:47 , processing array 9
2010-05-20 14:16:48 , processing array 10
2010-05-20 14:16:48 , processing array 11
2010-05-20 14:16:48 , processing array 12
2010-05-20 14:16:48 , processing array 13
2010-05-20 14:16:48 , processing array 14
2010-05-20 14:16:48 , processing array 15
2010-05-20 14:16:48 , processing array 16
2010-05-20 14:16:48 , processing array 17
2010-05-20 14:16:49 , processing array 18
2010-05-20 14:16:49 , processing array 19
2010-05-20 14:16:49 , processing array 20
2010-05-20 14:16:49 , processing array 21
> trans <- plotVST(lumi.T)
> dev.off()
null device
1
> pdf(plots_norm.pdf)
Error in gsub("%%", "", s) : object 'plots_norm.pdf' not found
> pdf("plots_norm.pdf")
> 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 2010-05-20 14:00:37 2010-05-20 14:01:08
2 2010-05-20 14:00:37 2010-05-20 14:01:08
3 2010-05-20 14:01:08 2010-05-20 14:01:08
4 2010-05-20 14:16:45 2010-05-20 14:16:49
5 2010-05-20 14:17:52 2010-05-20 14:17:53
6 2010-05-20 14:18:02 2010-05-20 14:18:02
command
1 lumiR.batch("raw_data_lumi_21.txt",
2 inputAnnotation = TRUE)
3 lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose = verbose)
4 lumiT(x.lumi = katie.lumi)
5 lumiN(x.lumi = lumi.T)
6 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
> plot(lumi.N.Q, what='density')
> plot(lumi.N.Q, what='boxplot')
>
> plot(lumi.N.Q, what='pair')
> plot(lumi.N.Q, what='MAplot')
> write.exprs(lumi.N.Q, file='normkatieData21_ann.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 KernSmooth_2.23-3 lattice_0.18-5
[5] Matrix_0.999375-38 nlme_3.1-96 tools_2.11.0 xtable_1.5-6
>
Best Wishes,
Katie
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