[BioC] affyQCReport with drosgenome2cdf

[Assa Yeroslaviz]

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
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