[Bioc-devel] [BioC] arrayQualityMetrics bug

Hi all,

I am having the same problem as Lavinia (below), namely, the
arrayQualityMetrics() function failing on Windows. I'm using code directly
from the vignette:

library("ALLMLL")
data("MLL.A")
library("arrayQualityMetrics")
arrayQualityMetrics(expressionset = MLL.A,

+ outdir = "MLL",
+ force = TRUE,
+ do.logtransform = TRUE)

The result is:

The report will be written into directory 'MLL'.
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
(loaded the KernSmooth namespace)
[[1]]

[[2]]

[[3]]

Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) :
   could not find function "svg"

traceback()

4: aqm.report.qm(p, obj[[i]], i, names(obj)[i])
3: aqm.writereport(reporttitle, expressionset, obj)
2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE,
        do.logtransform = TRUE)
1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE,
        do.logtransform = TRUE)

sessionInfo()

R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hgu133acdf_2.7.0          ALLMLL_1.2.8
  arrayQualityMetrics_3.2.3
[4] vsn_3.18.0                affyPLM_1.26.0
  preprocessCore_1.12.0
[7] gcrma_2.22.0              affy_1.28.0               Biobase_2.10.0


loaded via a namespace (and not attached):
  [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0
beadarray_2.0.2
  [5] Biostrings_2.18.2    DBI_0.2-5            genefilter_1.32.0
  grid_2.12.0
  [9] hwriter_1.3          IRanges_1.8.6        KernSmooth_2.23-4
  lattice_0.19-13
[13] latticeExtra_0.6-14  limma_3.6.9          marray_1.28.0
  RColorBrewer_1.0-2
[17] RSQLite_0.9-4        simpleaffy_2.26.1    splines_2.12.0
stats4_2.12.0
[21] survival_2.35-8      SVGAnnotation_0.7-2  tools_2.12.0
XML_3.2-0.2
[25] xtable_1.5-6

Thanks,
Dan


On Thu, Nov 18, 2010 at 11:14 PM, Lavinia Gordon<lavinia.gordon at mcri.edu.au

wrote:

  Hi Dan,
hmm, tried this, no luck:

arrayQualityMetrics(expressionset = methylumi.eset,outdir =

"arrayQualityMetrics_patients", force = TRUE)
The report will be written into directory 'arrayQualityMetrics_patients'.
[[1]]

[[2]]


Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) :
   could not find function "svg"

sessionInfo()

R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
  [1] arrayQualityMetrics_3.2.3 vsn_3.18.0
affyPLM_1.26.0            preprocessCore_1.12.0
  [5] gcrma_2.22.0              affy_1.28.0
SVGAnnotation_0.7-2       XML_3.2-0.1
  [9] Cairo_1.4-5               methylumi_1.4.0
lumi_2.2.0                Biobase_2.10.0

loaded via a namespace (and not attached):
  [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0
beadarray_2.0.1      Biostrings_2.18.0
  [6] DBI_0.2-5            genefilter_1.32.0    grid_2.12.0
hdrcde_2.15          hwriter_1.2
[11] IRanges_1.8.2        KernSmooth_2.23-4    lattice_0.19-13
latticeExtra_0.6-14  limma_3.6.4
[16] marray_1.28.0        MASS_7.3-8           Matrix_0.999375-45
mgcv_1.7-2           nlme_3.1-97
[21] RColorBrewer_1.0-2   RSQLite_0.9-3        simpleaffy_2.26.0
splines_2.12.0       stats4_2.12.0
[26] survival_2.36-1      xtable_1.5-6

Any ideas?
thanks
Lavinia.


On 19/11/2010 5:10 PM, Lavinia Gordon wrote:

Thanks Dan, sorry I had missed the previous posts.

On 19/11/2010 5:03 PM, Dan Tenenbaum wrote:



On Thu, Nov 18, 2010 at 9:51 PM, Lavinia Gordon<
lavinia.gordon at mcri.edu.au>  wrote:

Hi,
I think there is a problem with the 2.7 version of arrayQualityMetrics.
Following the example (in the script
\R\R-2.12.0\library\arrayQualityMetrics\scripts\arrayQualityMetrics.R)

library("arrayQualityMetrics")

Loading required package: affyPLM
Loading required package: gcrma
Loading required package: preprocessCore

Attaching package: 'affyPLM'

The following object(s) are masked from 'package:stats':

    resid, residuals, weights

Loading required package: vsn

arrayQualityMetrics(expressionset = MLL.A,

+                     outdir = "MLL",
+                     force = TRUE,
+                     do.logtransform = TRUE)
The directory 'MLL' has been created.
Error : cannot allocate vector of size 77.4 Mb
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
(loaded the KernSmooth namespace)
[[1]]

[[2]]

[[3]]

Error in aqm.report.qm(p, obj[[i]], i, names(obj)[i]) :
  could not find function "svg"
In addition: Warning message:
In arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force =
TRUE,  :
  Could not draw spatial distribution of intensities

traceback()

4: aqm.report.qm(p, obj[[i]], i, names(obj)[i])
3: aqm.writereport(reporttitle, expressionset, obj)
2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force =
TRUE,
       do.logtransform = TRUE)
1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force =
TRUE,
       do.logtransform = TRUE)

sessionInfo()

R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
  LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hgu133acdf_2.7.0          arrayQualityMetrics_3.2.0 vsn_3.18.0
        affyPLM_1.26.0
[5] preprocessCore_1.12.0     gcrma_2.22.0              ALLMLL_1.2.8
        affy_1.28.0
[9] Biobase_2.10.0

loaded via a namespace (and not attached):
  [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0
beadarray_2.0.1      Biostrings_2.18.0
  [6] DBI_0.2-5            genefilter_1.32.0    grid_2.12.0
  hwriter_1.2          IRanges_1.8.2
[11] KernSmooth_2.23-4    lattice_0.19-13      latticeExtra_0.6-14
  limma_3.6.4          marray_1.28.0
[16] RColorBrewer_1.0-2   RSQLite_0.9-3        simpleaffy_2.26.0
  splines_2.12.0       stats4_2.12.0
[21] survival_2.36-1      SVGAnnotation_0.6-0  tools_2.12.0
XML_3.2-0.1          xtable_1.5-6

with regards

Lavinia Gordon

  Hi Lavinia,

  This is a known issue that has come up with this package before on this
list. You need the current versions of arrayQualityMetrics (3.2.3) and
SVGAnnotation (0.7-2).
Try:
biocLite(c("arrayQualityMetrics","SVGAnnotation"))

  Dan



--
Senior Bioinformatics Officer
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road
Parkville
Victoria 3052
Australiawww.mcri.edu.au



--
Senior Bioinformatics Officer
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road
Parkville
Victoria 3052
Australiawww.mcri.edu.au

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