[BioC] Warnings after gcrma normalisation...

[James W. MacDonald]

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]]
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099