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@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




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