hello Steffi,
    In 'lumi' one needs to import the data out of BeadStudio in a particular
order of various columns (it can be arranged outside BS also). The columns
in order are-
1) TargetID
2) ProbeID (this is different from the Probe_ID col)
3) Avg_Signal
4) BEAD_STDER
5) Detection Pval
      These are the cols. that are mandatory. Apart from them, annotation
cols. can also be added. Info. about them is given in the "Using lumi.." pdf
that comes as vignette with the package.
    Also while importing the data using *lumiR* command, one needs to
specify the *grep* pattern of the column headers by which *lumiR* would
recognize which col. contains what. Though the deafult output has the
columns in order for *lumiR* to work in default settings, but just in case.
   I haven't analyzed HT-12 but WG-6. And above method works fine. *lumi*takes "
*ProbeID*" as the unique identifier (v 3.0 chips onward) and I didn't
encounter a 'duplicate ID..' message.
   I'm also unsure of the 'Inf' message. Maybe try importing the data with
specifications for most of the options, i.e. col. grep pattern.


regards
amit mandal

Graduate student
Genomics & Molecular Medicine lab
IGIB, Delhi


On Tue, Sep 8, 2009 at 7:30 PM, stefanie.figura <figura@uni-muenster.de>wrote:

> Dear all!
>
>
>
> I tried to analyse the Illumina HumanHT12 chip with the lumi package and I
> have some questions about the import and the results of the quality
> control.
>
>
>
> My first question is which columns have to be exported from BeadStudio at
> least? I am not sure because in the .pdf manual for the lumi package the
> figure is not  completely represented.
>
> I only exported ProbeID, PROBE_SEQUENCE (for nuID mapping with
> biocLite("lumiHumanAll.db")), AVG_Signal, BEAD_STDERR, Avg_NBEADS and
> Detection Pval from Group Gene Profile for all samples. Is there anything I
> missed which is
> <http://dict.leo.org/ende?lp=ende&p=thMx..&search=important> important for
> the analysis?
>
>
>
>
>
> I am not sure if I did a mistake in the code because of the results of the
> quality control:
>
>
>
> > importData <- lumiR("D:/Programme/eclipse/tmp/tmp_GroupProbeProfile.txt")
>
> Perform Quality Control assessment of the LumiBatch object ...
>
> Directly converting probe sequence to nuIDs ...
>
> Duplicated IDs found and were merged!
>
>
>
>
>
> > importData
>
> Summary of data information:
>
>       Data File Information:
>
>            BSGX Version      3.2.3
>
>            Report Date 9/8/2009 1:41:49 PM
>
>            Project     tmp
>
>            Group Set   all_seperated
>
>            Analysis    all_seperated_nonorm
>
>            Normalization     none
>
>
>
> Major Operation History:
>
>            submitted            finished
>
> 1 2009-09-08 15:44:37 2009-09-08 15:45:12
>
> 2 2009-09-08 15:45:12 2009-09-08 15:45:14
>
> 3 2009-09-08 15:45:34 2009-09-08 15:45:34
>
> 4 2009-09-08 15:45:14 2009-09-08 15:45:35
>
>
> command
>
> 1              lumiR("D:/Programme/eclipse/tmp/tmp_GroupProbeProfile.txt")
>
> 2        lumiQ(x.lumi = x.lumi, detectionTh = detectionTh, verbose =
> verbose)
>
> 3                                                  Subsetting 48803
> features.
>
> 4 addNuID2lumi(x.lumi = x.lumi, lib.mapping = lib.mapping, verbose =
> verbose)
>
>  lumiVersion
>
> 1      1.10.1
>
> 2      1.10.1
>
> 3      1.10.1
>
> 4      1.10.1
>
>
>
> Object Information:
>
> LumiBatch (storageMode: lockedEnvironment)
>
> assayData: 48802 features, 24 samples
>
>  element names: beadNum, detection, exprs, se.exprs
>
> phenoData
>
>  sampleNames: 4433719067_A, 4433719067_B, ..., 4433719068_L  (24 total)
>
>  varLabels and varMetadata description:
>
>    sampleID: The unique Illumina microarray Id
>
> featureData
>
>  featureNames: Ku8QhfS0n_hIOABXuE, fqPEquJRRlSVSfL.8A, ...,
> N8t5EuJCr0Tk9.zHno  (48802 total)
>
>  fvarLabels and fvarMetadata description:
>
>    ProbeID: The Illumina microarray identifier
>
> experimentData: use 'experimentData(object)'
>
> Annotation:
>
> Control Data: Available
>
> QC information: Please run summary(x, 'QC') for details!
>
>
>
>
>
> > summary(importData, 'QC')
>
> Data dimension:  48802 genes x 24 samples
>
>
>
> Summary of Samples:
>
>                        4433719067_A 4433719067_B 4433719067_C 4433719067_D
>
> mean                          6.8010       6.7230       6.6660       6.6870
>
> standard deviation            1.6760       1.6360       1.6370       1.6550
>
> detection rate(0.01)          0.3367       0.3432       0.3459       0.3436
>
> distance to sample mean          Inf          Inf          Inf          Inf
>
>                        4433719067_E 4433719067_F 4433719067_G 4433719067_H
>
> mean                          6.7220       6.6060        6.623       6.5730
>
> standard deviation            1.6470       1.6440        1.675       1.6440
>
> detection rate(0.01)          0.3531       0.3318        0.346       0.3378
>
> distance to sample mean          Inf          Inf          Inf          Inf
>
>                        4433719067_I 4433719067_J 4433719067_K 4433719067_L
>
> mean                          6.5400       6.5390       6.5470       6.4570
>
> standard deviation            1.6420       1.6740       1.6790       1.6390
>
> detection rate(0.01)          0.3316       0.3424       0.3464       0.3518
>
> distance to sample mean          Inf          Inf          Inf          Inf
>
>                        4433719068_A 4433719068_B 4433719068_C 4433719068_D
>
> mean                          6.3170       6.3000        6.304        6.213
>
> standard deviation            1.5630       1.5970        1.619        1.566
>
> detection rate(0.01)          0.3348       0.3257        0.336        0.320
>
> distance to sample mean          Inf          Inf          Inf          Inf
>
>                        4433719068_E 4433719068_F 4433719068_G 4433719068_H
>
> mean                           6.253       6.2510        6.169       6.2380
>
> standard deviation             1.600       1.6170        1.579       1.6590
>
> detection rate(0.01)           0.347       0.3434        0.335       0.3455
>
> distance to sample mean          Inf          Inf          Inf          Inf
>
>                        4433719068_I 4433719068_J 4433719068_K 4433719068_L
>
> mean                            -Inf        6.191       6.1420       6.0510
>
> standard deviation               NaN        1.642       1.6150       1.5360
>
> detection rate(0.01)          0.3319        0.346       0.3429       0.3462
>
> distance to sample mean      62.4000          Inf          Inf          Inf
>
>
>
>
>
> I wonder about the "Inf" and "NaN"  and I really think something was going
> wrong.
>
>
>
> Any advice is welcome, because I just started to learn R.
>
>
>
> Thank you very much in advance!
>
>
>
> Kind regards,
>
> Steffi
>
>
>        [[alternative HTML version deleted]]
>
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-- 
---------------------------------------------------------------
The robbed that smiles, steals something
from the thief.
 - Shakespeare
---------------------------------------------------------------



-- 
---------------------------------------------------------------
The robbed that smiles, steals something
from the thief.
- Shakespeare
---------------------------------------------------------------

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