[BioC] Does 'arrayQualityMetrics' package work with Affymetrix Human Exon 1.0 ST Arrays?
Wolfgang Huber
whuber at embl.de
Thu Apr 7 11:38:39 CEST 2011
Dear Nuria
generally, please use the (soon-to-be-released) devel version of
arrayQualityMetrics, it should deal more gracefully with your array type
and makes a much nicer report.
If there is no CDF file, the Affymetrix-specific quality metrics that
are based on probesets (NUSE, RLE, RNA 'digestion') will obviously not
work, but everyhing else should. Please let me know if you have any
problems with that (best to provide a small example dataset and the
script that you ran).
Best wishes
Wolfgang
Il Apr/6/11 3:37 PM, nqueralt at clinic.ub.es ha scritto:
> Dear all,
>
>
>
> I am testing the 'arrayQualityMetrics' package with .CEL files obtained with Affymetrix Human Exon 1.0 ST Arrays as raw data. But, even though i got an html Qmreport, i also got these errors during the process on R:
>
>
>
>> Data<- ReadAffy()
>
>> Data at cdfName
>
> [1] "HuEx-1_0-st-v2"
>
>> Data
>
> AffyBatch object
>
> size of arrays=2560x2560 features (17 kb)
>
> cdf=HuEx-1_0-st-v2 (??? affyids)
>
> number of samples=2
>
> Error in getCdfInfo(object) :
>
> Could not obtain CDF environment, problems encountered:
>
> Specified environment does not contain HuEx-1_0-st-v2
>
> Library - package huex10stv2cdf not installed
>
> Bioconductor - huex10stv2cdf not available
>
> In addition: Warning message:
>
> missing cdf environment! in show(AffyBatch)
>
>> arrayQualityMetrics(expressionset = Data,outdir = "rawData_AQM",force = TRUE,d o.logtransform = TRUE)
>
> The report will be written into directory 'rawData_AQM'.
>
> Error in getCdfInfo(object) :
>
> Could not obtain CDF environment, problems encountered:
>
> Specified environment does not contain HuEx-1_0-st-v2
>
> Library - package huex10stv2cdf not installed
>
> Bioconductor - huex10stv2cdf not available
>
> Error in fitPLM(pp1, background = FALSE, normalize = FALSE) :
>
> argument is try-error fitPLM requires AffyBatch
>
> Error in aqm.rle(expressionset, dataprep, affyproc, intgroup = intgroup) :
>
> trying to get slot "model.description" from an object (class "try-error") that is not an S4 object
>
> In addition: Warning message:
>
> In aqm.prepaffy(expressionset) :
>
> RLE and NUSE plots from the package 'affyPLM' cannot be produced for this data set.
>
> Error in aqm.nuse(expressionset, dataprep, affyproc, intgroup = intgroup) :
>
> trying to get slot "model.description" from an object (class "try-error") that is not an S4 object
>
> Error in getCdfInfo(object) :
>
> Could not obtain CDF environment, problems encountered:
>
> Specified environment does not contain HuEx-1_0-st-v2
>
> Library - package huex10stv2cdf not installed
>
> Bioconductor - huex10stv2cdf not available
>
> KernSmooth 2.23 loaded
>
> Copyright M. P. Wand 1997-2009
>
> (loaded the KernSmooth namespace)
>
> [[1]]
>
>
>
> Error in getCdfInfo(object) :
>
> Could not obtain CDF environment, problems encountered:
>
> Specified environment does not contain HuEx-1_0-st-v2
>
> Library - package huex10stv2cdf not installed
>
> Bioconductor - huex10stv2cdf not available
>
>>
>
>
>
>
>
> For more info:
>
>
>
>> sessionInfo()
>
> R version 2.12.2 (2011-02-25)
>
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
>
>
> locale:
>
> [1] LC_CTYPE=en_US.ISO-8859-1 LC_NUMERIC=C
>
> [3] LC_TIME=en_US.ISO-8859-1 LC_COLLATE=en_US.ISO-8859-1
>
> [5] LC_MONETARY=C LC_MESSAGES=en_US.ISO-8859-1
>
> [7] LC_PAPER=en_US.ISO-8859-1 LC_NAME=C
>
> [9] LC_ADDRESS=C LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.ISO-8859-1 LC_IDENTIFICATION=C
>
>
>
> attached base packages:
>
> [1] stats graphics grDevices datasets utils methods base
>
>
>
> other attached packages:
>
> [1] arrayQualityMetrics_3.2.4 vsn_3.18.0
>
> [3] affyPLM_1.26.1 preprocessCore_1.12.0
>
> [5] gcrma_2.22.0 affy_1.28.0
>
> [7] Biobase_2.10.0 R.utils_1.7.4
>
> [9] R.oo_1.8.0 R.methodsS3_1.2.1
>
>
>
> loaded via a namespace (and not attached):
>
> [1] affyio_1.18.0 annotate_1.28.1 AnnotationDbi_1.12.0
>
> [4] beadarray_2.0.5 Biostrings_2.18.4 DBI_0.2-5
>
> [7] genefilter_1.32.0 grid_2.12.2 hwriter_1.3
>
> [10] IRanges_1.8.9 KernSmooth_2.23-4 lattice_0.19-17
>
> [13] latticeExtra_0.6-14 limma_3.6.9 marray_1.28.0
>
> [16] RColorBrewer_1.0-2 RSQLite_0.9-4 simpleaffy_2.26.1
>
> [19] splines_2.12.2 stats4_2.12.2 survival_2.36-5
>
> [22] SVGAnnotation_0.9-0 tools_2.12.2 XML_3.2-0
>
> [25] xtable_1.5-6
>
>
>
> It seems that there is some kind of problem with the AffyBatch object i generated (called 'Data' in the example attached). The problem could be the annotation? I also searched for the 'huex10stv2cdf' package unsuccessfully.
>
> In a normal html report with Affymetrix arrays i obtained:
>
>
>
> * Section 1: Individual array quality<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S1#S1> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S1#S1>
>
> * MA plots
> * Spatial distribution of feature intensities
>
>
>
> * Section 2: Array intensity distributions<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S2#S2> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S2#S2>
>
> * Boxplots
> * Density plots
> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S3#S3>
>
> * Section 3: Between array comparison<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S3#S3> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S3#S3>
>
> * Heatmap representation of the distances between arrays
> * Principal Component Analysis
>
>
>
> * Section 4: Variance mean dependence<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S4#S4> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S4#S4>
>
> * Standard deviation versus rank of the mean
>
>
>
> * Section 5: Affymetrix specific plots<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S5#S5> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM_Affy\QMreport.html#S5#S5>
>
> * RNA digestion plot
> * Relative Log Expression plot
> * Normalized Unscaled Standard Error (NUSE) plot
> * Diagnostic plot recommended by Affymetrix
> * Perfect matches and mismatches
>
> And with the exon array:
>
>
>
> * Section 1: Individual array quality<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM\QMreport.html#S1#S1> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM\QMreport.html#S1#S1>
>
> * MA plots
> * Spatial distribution of feature intensities
>
>
>
> * Section 2: Array intensity distributions<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM\QMreport.html#S2#S2> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM\QMreport.html#S2#S2>
>
> * Boxplots
> * Density plots
>
>
>
> * Section 3: Between array comparison<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM\QMreport.html#S3#S3> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM\QMreport.html#S3#S3>
>
> * Heatmap representation of the distances between arrays
> * Principal Component Analysis
>
>
>
> * Section 4: Variance mean dependence<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM\QMreport.html#S4#S4> <file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM\QMreport.html#S4#S4>
>
> * Standard deviation versus rank of the mean
>
>
>
> * Section 5: Affymetrix specific plots<file:///C:\Documents%20and%20Settings\nqueralt.HCP\Escritorio\rawData_AQM\QMreport.html#S5#S5>
>
>
>
> Nothing in the last section as you can see. The rest of the sections look normal. What am i doing wrong?
>
>
>
>
>
> Many thanks in advance!
>
>
>
> Regards,
>
>
>
> -------------------------------------------------------
> Núria
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
>
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--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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