[BioC] Does 'arrayQualityMetrics' package work with Affymetrix Human Exon 1.0 ST Arrays?
James W. MacDonald
jmacdon at med.umich.edu
Wed Apr 6 16:04:26 CEST 2011
Hi Núria,
The arrayQualityMetrics package relies on the affy and simpleaffy
packages for much of the data processing. Unfortunately, neither of
these packages is designed for a non 3'-biased array like the exon chip.
You want to use either oligo or xps for these data, or if you want to go
off-campus, the aroma.affymetrix package will work as well.
Best,
Jim
On 4/6/2011 9:37 AM, nqueralt at clinic.ub.es wrote:
> 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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--
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
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