[BioC] Should AgiMicroRna and GeneSpring quantile normalisation's results be the same ?
Martin Morgan
mtmorgan at fhcrc.org
Mon Aug 13 15:47:42 CEST 2012
On 08/13/2012 06:24 AM, Seyit Ali KAYIS wrote:
> Hi again,
>
> (I realized that attachment is not allowed. So I have copied my email
> and summarized the result in the table below Sorry for duplication).
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Also I'm cc'ing the packageDescription("AgiMicroRna")$Maintainer, as
they are perhaps in the best position to provide specific answers.
It sounds like you are on the way to identifying specific examples where
the algorithms differ, which is the right direction for identifying
simple reproducible examples that others can comment on.
Martin
>
> Thanks for the comments (BTW: Still waiting for comments, from
> AgiMicroRNA-GeneSpring users, if any one had similar experience and
> would like to share their solutions etc.).
>
> Meanwhile, I just checked correlation between quantile normalization
> results of GeneSpring and AgiMicroRna and wanted to share the results
> with you and others. 235 miRNA were expressed at least in one individual.
>
>
> Correlation N
> <0.5 3
> 0.5-0.9 6
> 0.9-0.989 46
> 0.99-1 179
> 1 1
>
>
> Kind Regards
>
> Seyit Ali
>
>
>
>
> On 12/08/2012 2:12 PM, Paul Geeleher wrote:
>> Quantiles normalization is an incredibly simple algorithm, so I'm not
>> sure why there should be differences. Perhaps one platform has ignored
>> some of the probes (i.e. background probes or control probes)?
>> Although this might not be documented. I would say though, that if the
>> across sample correlations for each gene are very high (i.e. > .99)
>> for most of the genes, then you probably don't have anything to worry
>> about.
>>
>> Paul.
>>
>> On Sat, Aug 11, 2012 at 11:24 PM, Seyit Ali KAYIS
>> <skayis at selcuk.edu.tr> wrote:
>>> Dear All,
>>>
>>> I have microRNA microaaray expression data from Agilent platform
>>> exported by
>>> the Agilent Feature Extraction (AFE) image analysis software.
>>> Initially, we
>>> performed quantile normalisation using GeneSpring (version 12.1)
>>> software
>>> (demo version). Being an R user, I wanted to do rest of the analysis by
>>> using R. So, I repeated quantile normalisation using "AgiMicroRna"
>>> library.
>>> Before further analysis, I compared raw ( gTotalProbeSignal(raw) from
>>> GeneSpring and ddTGS$TGS from AgiMicroRNA) and quantile normalised (
>>> gTotalProbeSignal(normalized) from GeneSpring and ddNORM$TGS from
>>> AgiMicroRNA ) output of two softwares. Raw output of two softwares
>>> are the
>>> same. However, there are some differences in the some of the quantile
>>> normalised output, although majority of the output are very similar. I
>>> suppose GeneSpring and "AgiMicroRna" are using the same algorithm
>>> and they
>>> should produce the same results. I was wondering whether I am doing
>>> something wrong during the procees? Does any one faced similar
>>> situation?
>>>
>>> My sessionInfo() and steps I am following in AgiMicroRna are below.
>>>
>>> Any comment, help deeply appreciated.
>>>
>>> Kind Regards
>>>
>>> Seyit Ali
>>>
>>> ============================================================================
>>>
>>> ==============
>>>
>>>> sessionInfo()
>>> R version 2.15.1 (2012-06-22)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
>>> LC_MONETARY=English_Australia.1252
>>> [4] LC_NUMERIC=C LC_TIME=English_Australia.1252
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] AgiMicroRna_2.6.0 affycoretools_1.28.0 KEGG.db_2.7.1
>>> GO.db_2.7.1 RSQLite_0.11.1
>>> [6] DBI_0.2-5 AnnotationDbi_1.18.1 preprocessCore_1.18.0
>>> affy_1.34.0 limma_3.12.1
>>> [11] Biobase_2.16.0 BiocGenerics_0.2.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affyio_1.24.0 annaffy_1.28.0 annotate_1.34.1
>>> BiocInstaller_1.4.7 biomaRt_2.12.0 Biostrings_2.24.1
>>> [7] Category_2.22.0 gcrma_2.28.0 genefilter_1.38.0
>>> GOstats_2.22.0 graph_1.34.0 grid_2.15.1
>>> [13] GSEABase_1.18.0 IRanges_1.14.4 lattice_0.20-6
>>> RBGL_1.32.1
>>> RCurl_1.91-1.1 splines_2.15.1
>>> [19] stats4_2.15.1 survival_2.36-14 tools_2.15.1
>>> XML_3.9-4.1
>>> xtable_1.7-0 zlibbioc_1.2.0
>>>
>>> ============================================================================
>>>
>>> ============
>>>
>>> "AgiMicroRna" steps
>>>
>>>
>>> library(AgiMicroRna)
>>>
>>> sessionInfo()
>>>
>>> AFE.TGS = TRUE
>>>
>>> half= FALSE # ddTGS signal with 'half method'
>>> offset=0
>>> makePLOT=FALSE
>>>
>>>
>>> # NORMALIZATION of ddTGS
>>> NORMmethod="quantile"
>>> makePLOTpre=TRUE
>>> makePLOTpost=TRUE
>>>
>>> # FILTERING PROBES
>>> control = TRUE
>>> IsGeneDetected = TRUE
>>> wellaboveNEG = FALSE
>>> limIsGeneDetected = 50
>>> limNEG = 25
>>> makePLOT = FALSE
>>>
>>> # READING THE Target File
>>> targets=readTargets(infile="targets.txt",verbose=TRUE)
>>> # READING THE DATA (RGList)
>>> dd=readMicroRnaAFE(targets,verbose=TRUE)
>>> names(dd)
>>>
>>>
>>> # PRE-PROCESSING # USING AFE gTotalGeneSignal & # NORMALIZATION
>>> # tgsMicroRna: creates an uRNAList object that contains the Total Gene
>>> Signal computed
>>> # by the Agilent Feature Extraction algorithms
>>> # tgsNormalization: creates an uRNAList object containing the
>>> Normalized
>>> Total
>>> # Gene Signal in log 2 scale
>>>
>>> if(AFE.TGS) {
>>> message('pre-processing: AFE TGS')
>>> cat('\n')
>>> ddTGS = tgsMicroRna(dd, half = FALSE, makePLOT = FALSE,verbose = FALSE)
>>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = FALSE,
>>> makePLOTpost = FALSE, targets, verbose = TRUE)
>>> }
>>>
>>> # Obtaining raw data
>>>
>>> TGSTGS<-cbind(ddTGS$genes, ddTGS$TGS)
>>>
>>> # Obtaining quantile normalised data
>>>
>>> NormData<-cbind(ddNORM$genes, ddNORM$TGS)
>>>
>>> ============================================================================
>>>
>>> =====
>>>
>>>
>>>
>>> --------------------------------------------------------
>>> Dr. Seyit Ali KAYIS
>>> Selcuk University, Faculty of Agriculture
>>> Kampus/Konya, Turkey
>>>
>>> skayis at selcuk.edu.tr, s_a_kayis at yahoo.com, s_a_kayis at hotmail.com
>>>
>>> Tel: +90 332 223 2830 Mobile: +90 535 587 1139
>>>
>>> Greetings from Konya, Turkey
>>> http://www.ziraat.selcuk.edu.tr/skayis/
>>> --------------------------------------------------------
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
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>>
>>
>
>
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