[BioC] help with lumi
Gilbert Feng
g-feng at northwestern.edu
Fri May 21 03:15:37 CEST 2010
Hi, Katie
When you set inputAnnotation to TRUE, you have to specify annotationColumn.
The lumi.R manual page states :" they can set the parameter
"inputAnnotation" as TRUE. At the same time, they can also specify which
columns to be inputted by setting parameter "annotationColumn"."
You can use lumiHumanAll.db to map nuIDs in your lumi object to any other
IDs.
Gilbert
On 5/20/10 8:25 AM, "Taylor, Katie" <kt70 at leicester.ac.uk> wrote:
> 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
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> 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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