Warnings after gcrma normalisation...
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Bas Jansen ▴ 150
@bas-jansen-2966
Last seen 7.1 years ago
Hi, I am importing microarray data, and after normalization with gcrma I get the following warnings: <quote/> Warning messages: 1: replacing previous import by ‘utils::head’ when loading ‘mouse4302cdf’ 2: replacing previous import by ‘utils::tail’ when loading ‘mouse4302cdf’ </quote> Should I be concerned, and if so, can something be done to prevent this? I am on Mavericks (Mac OSX), on a Macbook Pro from early 2011. Further info about the session: > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] mouse4302probe_2.14.0 AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2 [4] mouse4302cdf_2.14.0 inSilicoMerging_1.8.0 inSilicoDb_2.0.1 [7] RCurl_1.95-4.1 bitops_1.0-6 rjson_0.2.13 [10] DWD_0.11 Matrix_1.1-3 gcrma_2.36.0 [13] affy_1.42.0 limma_3.20.1 Biobase_2.24.0 [16] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] affyio_1.32.0 BiocInstaller_1.14.1 Biostrings_2.32.0 [4] DBI_0.2-7 grid_3.1.0 IRanges_1.22.3 [7] lattice_0.20-29 preprocessCore_1.26.0 RSQLite_0.11.4 [10] splines_3.1.0 stats4_3.1.0 tools_3.1.0 [13] XVector_0.4.0 zlibbioc_1.10.0 Thanks and kind regards, Bas [[alternative HTML version deleted]]
Microarray Normalization gcrma Microarray Normalization gcrma • 1.3k views
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@james-w-macdonald-5106
Last seen 7 hours ago
United States
Hi Bas, On 4/18/2014 9:37 AM, Bas Jansen wrote: > Hi, > > I am importing microarray data, and after normalization with gcrma I get > the following warnings: > > <quote/> > Warning messages: > 1: replacing previous import by ???utils::head??? when loading ???mouse4302cdf??? > 2: replacing previous import by ???utils::tail??? when loading ???mouse4302cdf??? > </quote> > > Should I be concerned, and if so, can something be done to prevent this? There is no need to be concerned, and you cannot prevent this. For some background, these days R uses a namespace to control what functions are exported from a given package. This functionality also allows a package to import functions from other packages without explicitly attaching them. This is what you see when you get the output from sessionInfo() (see below under the heading 'loaded via a namespace (and not attached)'). What is happening is that an earlier package you loaded (looks like AnnotationDbi) is loading the namespace for the utils package, and then mouse4302cdf is importing it again, and the warning is just informing you of that fact. Not sure why it just mentions two specific functions (there are 202 functions being imported in total). But long story short, it's not a problem. Best, Jim > I am on Mavericks (Mac OSX), on a Macbook Pro from early 2011. Further info > about the session: > >> sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] mouse4302probe_2.14.0 AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2 > [4] mouse4302cdf_2.14.0 inSilicoMerging_1.8.0 inSilicoDb_2.0.1 > [7] RCurl_1.95-4.1 bitops_1.0-6 rjson_0.2.13 > [10] DWD_0.11 Matrix_1.1-3 gcrma_2.36.0 > [13] affy_1.42.0 limma_3.20.1 Biobase_2.24.0 > [16] BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.32.0 BiocInstaller_1.14.1 Biostrings_2.32.0 > [4] DBI_0.2-7 grid_3.1.0 IRanges_1.22.3 > [7] lattice_0.20-29 preprocessCore_1.26.0 RSQLite_0.11.4 > [10] splines_3.1.0 stats4_3.1.0 tools_3.1.0 > [13] XVector_0.4.0 zlibbioc_1.10.0 > > Thanks and kind regards, > Bas > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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