[BioC] Unable to \'standardise\' logtransformed dataset of contrasts using Mfuzz package

[Matthias Futschik]

Dear Franklin,
it looks like that your numbers are in fact characters
> head(wCA12m)

             CA.2wk11.H11   CA.4wk11.CA.2wk11 CA.8wk11.CA.4wk11 CA.12wk11.CA.8wk11
123.1166295 " 0.018961357" "-0.091637119"    " 3.268257162"    "-1.025643391"
109.1012434 " 0.146168274" "-0.055655014"    " 3.172041095"    "-0.969301615"


since quotation marks are appearing.
Once you convert them in real numbers, it should be ok.

hth,
Matthias.


Em 26-06-2013 22:17, FRANKLIN JOHNSON [guest] escreveu:
> Dear Maintainer,
>
> I'm analyzing metabolomic LC-MS intensity values.
> To reduced these large numbers, I log transformed the dataset. To replace any Inf/-Inf/NA with a zero:
>> logtransfo[!is.finite(logtransfo)]<-0
> and checked for NAs:
>> is.na(logtransfo))
>              CA.2wk11.H11 CA.4wk11.CA.2wk11 CA.8wk11.CA.4wk11 CA.12wk11.CA.8wk11
> 123.1166295        FALSE             FALSE             FALSE              FALSE
> 109.1012434        FALSE             FALSE             FALSE              FALSE
>
> All cells printed FALSE.
> I made contrasts using limma package.
>> head(wCA12m)
>              CA.2wk11.H11   CA.4wk11.CA.2wk11 CA.8wk11.CA.4wk11 CA.12wk11.CA.8wk11
> 123.1166295 " 0.018961357" "-0.091637119"    " 3.268257162"    "-1.025643391"
> 109.1012434 " 0.146168274" "-0.055655014"    " 3.172041095"    "-0.969301615"
>
> Made an expression set:
>> wCA12me
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 124 features, 4 samples
>    element names: exprs
> protocolData: none
> phenoData: none
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation:
>
> is.na(exprs(wCA12me))
>              CA.2wk11.H11 CA.4wk11.CA.2wk11 CA.8wk11.CA.4wk11 CA.12wk11.CA.8wk11
> 123.1166295        FALSE             FALSE             FALSE              FALSE
> 109.1012434        FALSE             FALSE             FALSE              FALSE
>
> I loaded library(Mfuzz), and went through the steps as indicated in the manual.
>
>> wCA12me.r=filter.NA(wCA12me)
> 0 genes excluded.
>> wCA12me.f=fill.NA(wCA12me.r, mode="knn") #after failing to standardise, I also tried using the other mode options.
> I could get a nice plot with "knn" and "knnw", but using "mean" and "median" gave an error for fill.NA.
>
>> tmp=filter.std(wCA12me, min.std=0)
> 0 genes excluded.
>
> Also, changed the min.std value.
>> tmp=filter.std(wCA12me, min.std=2)
> 67 genes excluded.
>
> For either case of changing the mode="", and min.std="",
> I always get the same error message when using the call to 'standardise':
>
>> wCA12me.s=standardise(wCA12me.f)
> Error in data[i, ] - mean(data[i, ], na.rm = TRUE) :
>    non-numeric argument to binary operator
> In addition: Warning message:
> In mean.default(data[i, ], na.rm = TRUE) :
>    argument is not numeric or logical: returning NA
>
> Checking my file several times, I showed that no data points contain NA. I think I understand what the error is saying, but I didn't expect negative values to affect
> the clustering algorithm. I was able to complete the package with non-transformed values, however, the transformed values give slightly different results, and wanted to compare the non-transformed and log-transformed datasets.
>
> This being LC-MS metabolomic data, could I use a different function to transform the data to not get negative values?
>
> Thanks for your attention.
> Regards,
> Franklin
>
>
>
>
>   -- output of sessionInfo():
>
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] tcltk     parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] limma_3.16.5         Mfuzz_2.18.0         DynDoc_1.38.0
> [4] widgetTools_1.38.0   e1071_1.6-1          class_7.3-7
> [7] Biobase_2.20.0       BiocGenerics_0.6.0   BiocInstaller_1.10.2
>
> loaded via a namespace (and not attached):
> [1] tkWidgets_1.38.0 tools_3.0.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
>


-- 
************************************************************
Dr. Matthias E. Futschik
Principal Investigator in Systems Biology and Bioinformatics
Centre for Molecular and Structural Biomedicine
University of Algarve, Campus of Gambelas
8005-139 Faro, Portugal
url: www.sysbiolab.eu
email: mfutschik at ualg.pt