[BioC] affyQCReport with drosgenome2cdf
Wolfgang Huber
whuber at embl.de
Sun Nov 21 14:51:13 CET 2010
Hi Assa
are you using the updated version of 'arrayQualityMetrics'? (see:
https://stat.ethz.ch/pipermail/bioconductor/2010-November/036459.html )
What is for you the result of
nrow(rawData) ?
(The function assumes that 'nrow' and 'ncol' applied to the data object
provide the correct spatial coordinates)
I suspect that the spatial plot (sub)function does not work for some
array types. However, you should get a report containing all the other
types of report sections. And I hope the spatial plots can be fixed for
the next release.
Best wishes
Wolfgang
Il Nov/16/10 8:37 AM, Assa Yeroslaviz ha scritto:
> Hi Jim, Bioconductor users
>
> thanks for the note. I tried the package and it looks good.
>
> Unfortunately i get some error messages when analysinf the raw data.
>
>> rawData<- ReadAffy(widget=T) # creating the affybatch from CEL files.
>>
>> arrayQualityMetrics(rawData, "data_raw", force= TRUE, do.logtransform= TRUE) # QC of raw data
> The directory 'data_raw' has been created.
> Error in seq_len(maxr) :
> argument must be coercible to non-negative integer
> KernSmooth 2.23 loaded
> Copyright M. P. Wand 1997-2009
> (loaded the KernSmooth namespace)
> [[1]]
>
> [[2]]
>
> Warning message:
> In arrayQualityMetrics(rawData, "data_raw", force = TRUE,
> do.logtransform = TRUE) :
> Could not draw spatial distribution of intensities
>
> Error in sfs(x) :
> error in evaluating the argument 'object' in selecting a method for
> function 'sfs'
>
> But after normalizing the datausing the gcRMA algorithm I don't get
> these errors.
>
>> normData<- gcrma(rawData) # GC-RMA normalization
> Adjusting for optical effect............Done.
> Computing affinitiesLoading required package: AnnotationDbi
> .Done.
> Adjusting for non-specific binding............Done.
> Normalizing
> Calculating Expression
> Warning message:
> closing unused connection 3 (QMreport.html)
>> arrayQualityMetrics(normData, "data_norm", force= TRUE, do.logtransform= TRUE) # QC of normalized data (after RMA)
> The directory 'data_norm' has been created.
> [[1]]
>
> [[2]]
>
>>
>
>
> Does anyone has an idea as to what these errors means?
> I read in the mailing lists, that the spatial dist. is quite a memory
> consuming procedure, but I am using a 64Bit Unix server (Ubuntu) with
> 48GB RAM. So I don't think that can be a problem.
> Beside I don't understand the other errors.
>
> I do get as a result a list of images as I suppose. I just want to
> make sure, that these error messages have nothing to do with the
> results themselves.
>
> I hope someone can explain them in short.
>
> Thanks
>
> Assa
>
> On Mon, Nov 15, 2010 at 15:12, James W. MacDonald<jmacdon at med.umich.edu> wrote:
>> Hi Assa,
>>
>> You might try the arrayQualityMetrics package.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> On 11/15/2010 4:59 AM, Assa Yeroslaviz wrote:
>>>
>>> Hi everybody,
>>>
>>> I have a set of drosophile genome 2.0 arrays to analyze. I wanted to
>>> start with a quality control using the affyQCReport package.
>>>
>>> according to the manual I set the enivironment.
>>>>
>>>> setQCEnvironment("drosgenome2cdf",
>>>> "/home/AYeroslaviz/R/x86_64-pc-linux-gnu-library/2.12/simpleaffy/extdata")
>>>
>>> and run the QCreport on the raw data
>>>>
>>>> QCReport(rawData)
>>>
>>> unfortunately I get an error message
>>>
>>> Error: NAs in foreign function call (arg 5)
>>>
>>> Can someone please tell me what the meaning of this error. I tried to
>>> search the mailing lists but didn't find anything.
>>> If AffyQCReport doesn't work, do I have an alternative?
>>>
>>> Thanks
>>>
>>> Assa
>>>
>>>> sessionInfo()
>>>
>>> R version 2.12.0 (2010-10-15)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] tools tcltk splines stats graphics grDevices utils
>>> [8] datasets methods base
>>>
>>> other attached packages:
>>> [1] simpleaffy_2.26.0 genefilter_1.32.0
>>> [3] drosophila2cdf_2.7.0 arrayQualityMetrics_3.2.1
>>> [5] vsn_3.18.0 affyPLM_1.26.0
>>> [7] gcrma_2.22.0 tkWidgets_1.28.0
>>> [9] widgetTools_1.28.0 siggenes_1.24.0
>>> [11] multtest_2.6.0 samr_1.28
>>> [13] impute_1.24.0 MASS_7.3-5
>>> [15] vioplot_0.2 sm_2.2-4.1
>>> [17] preprocessCore_1.10.0 DynDoc_1.28.0
>>> [19] cluster_1.13.1 affydata_1.11.10
>>> [21] affycomp_1.26.0 affyQCReport_1.28.0
>>> [23] lattice_0.19-13 affy_1.28.0
>>> [25] Biobase_2.10.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affyio_1.16.0 annotate_1.28.0 AnnotationDbi_1.12.0
>>> [4] beadarray_2.0.2 Biostrings_2.18.0 DBI_0.2-5
>>> [7] grid_2.12.0 hwriter_1.2 IRanges_1.8.2
>>> [10] latticeExtra_0.6-14 limma_3.6.6 marray_1.28.0
>>> [13] RColorBrewer_1.0-2 RSQLite_0.9-1 stats4_2.12.0
>>> [16] survival_2.35-8 SVGAnnotation_0.7-2 XML_2.6-0
>>> [19] xtable_1.5-6
>>>
>>> _______________________________________________
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>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be
>> used for urgent or sensitive issues
>>
>
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