Hi Jim,
Thanks for your answer, it's my first experience with Affy data, I used to
work with Agilent before.
I take a look at the vignette and generated the requested file based on the
info about the htmg430pm data :
array htmg430pmcdf
alpha1 0.05
alpha2 0.065
spk bioB AFFX-r2-Ec-bioB-3_at
spk bioC AFFX-r2-Ec-bioC-3_at
spk bioD AFFX-r2-Ec-bioD-3_at
spk creX AFFX-r2-P1-cre-3_at
ratio actin3/actin5 AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_5_at
ratio actin3/actinM AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_M_at
ratio gapdh3/gapdh5 AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_5_at
ratio gapdh3/gapdhM AFFX-GapdhMur/M32599_3_at AFFX-GapdhMur/M32599_M_at

report works well for normalized data, but for raw data i get the following
errors:

The report will be written in directory 'report'.
Error : NAs in foreign function call (arg 1)
Error in density.default(as.matrix(log2(mm(expressionset))), ...) :
  'x' contains missing values
In addition: Warning message:
In aqm.qcstats(expressionset) :
  'plot(qcStats)' from the package 'simpleaffy' failed for this dataset.
Error in obj[[i]]$legend : $ operator is invalid for atomic vectors
In addition: Warning message:
In arrayQualityMetrics(aBatch, outdir = "report") :
  Cannot draw the Perfect Match versus MisMatch plot

here's the code i'm using :

#  Identify CEL files.
fls <- list.files("/", ".*CEL")
# Input raw data
aBatch <- ReadAffy(filenames = fls)
# Process CEL files using RMA (robust multi-array average).
eset <- justRMA(filenames = fls)

arrayQualityMetrics(aBatch,outdir = "report_raw")
arrayQualityMetrics(eset,outdir = "report_normalized")


Any idea about what is wrong with the QC report on raw data ?
Thanks in advance.

Regards,
Ramzi








Best,
Ramzi
----------------------------------------------------------------


On Mon, Jan 11, 2010 at 2:52 PM, James W. MacDonald
<jmacdon@med.umich.edu>wrote:

> Hi Ramzi,
>
>
> Ramzi TEMANNI wrote:
>
>> Hi,
>> I'm runing some QC analysis with 5 Affy mouse genechip HT430PM
>> I've installed the required libraries(affy, arrayQualityMetrics,
>> htmg430pmcdf) and all dependecies
>> I'm using the following code:
>> fls <- list.files("/", ".*CEL")
>> eset <- justRMA(filenames = fls)
>> aBatch <- ReadAffy(filenames = fls)
>> arrayQualityMetrics(aBatch,outdir = "report")
>>
>> The last commad shows the following error message:
>>
>> The report will be written in directory 'report'.
>> Error in setQCEnvironment(cdfn) :
>>  Could not find array definition file ' htmg430pmcdf.qcdef '. Simpleaffy
>> does not know the QC parameters for this array type.
>> See the package vignette for details about how to specify QC parameters
>> manually.
>>
>
> This seems pretty clear to me. The simpleaffy package does not have the QC
> parameters for this array and there is some explanation of how to fix this
> in the package vignette. Did you look in the package vignette to see how to
> fix it?
>
> Note that the htmg430pm chip is quite similar to the moe430 chip, so the QC
> parameters will likely be the same, but you might need to adjust the names
> of the QC probes.
>
> Best,
>
> Jim
>
>
>> Error in density.default(as.matrix(log2(mm(expressionset))), ...) :
>>  'x' contains missing values
>> In addition: Warning message:
>> In aqm.qcstats(expressionset) :
>>  'plot(qcStats)' from the package 'simpleaffy' failed for this dataset.
>> Error in obj[[i]]$legend : $ operator is invalid for atomic vectors
>> In addition: Warning message:
>> In arrayQualityMetrics(aBatch, outdir = "report") :
>>  Cannot draw the Perfect Match versus MisMatch plot
>>
>> Any idea about the orgin of this error ?
>> Thanks in advance for your help.
>> Kind regards
>> Ramzi
>> ----------------------------------------------------------------
>>
>>  sessionInfo()
>>>
>> R version 2.10.1 (2009-12-14)
>> x86_64-pc-linux-gnu
>> 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] stats     graphics  grDevices utils     datasets  methods   base
>> other attached packages:
>> [1] arrayQualityMetrics_2.4.3 affyPLM_1.22.0
>> [3] preprocessCore_1.8.0      gcrma_2.18.0
>> [5] htmg430pmcdf_2.5.0        affy_1.24.2
>> [7] Biobase_2.6.1
>> loaded via a namespace (and not attached):
>>  [1] affyio_1.14.0       annotate_1.24.0     AnnotationDbi_1.8.1
>>  [4] beadarray_1.14.0    Biostrings_2.14.8   DBI_0.2-4
>>  [7] genefilter_1.28.2   grid_2.10.1         hwriter_1.1
>> [10] IRanges_1.4.9       lattice_0.17-26     latticeExtra_0.6-4
>> [13] limma_3.2.1         marray_1.24.0       RColorBrewer_1.0-2
>> [16] RSQLite_0.7-3       simpleaffy_2.22.0   splines_2.10.1
>> [19] stats4_2.10.1       survival_2.35-8     tcltk_2.10.1
>> [22] tools_2.10.1        vsn_3.14.0          xtable_1.5-6
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> --
> 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
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be
> used for urgent or sensitive issues
>

	[[alternative HTML version deleted]]

