[BioC] QCReport: specifying alt CDF (MoGene-1_0-st-v1)?

Tue Sep 21 00:20:50 CEST 2010

Hi BioC 

(sessionInfo() at bottom)

I'm trying to help a group here do some QC on their affy datasets 
derived from the mogene10stv1 array set.  This array is not in 
mainstream BioC support but I've created and installed the CDF 
environment for that array:

>  make.cdf.package("MoGene-1_0-st-v1.r3.cdf", species = "Mus_mus")
(completes, and I've installed the generated CDF env)

but when I try to run  QCReport on this dataset (even explicitly 
specifying the mogene10stv1 CDF env), I get the errors:

> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1cdf"))
#   or 
> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1"))   
#   (get same error)

Error: NAs in foreign function call (arg 1)
In addition: Warning messages:
1: In data.row.names(row.names, rowsi, i) :
  some row.names duplicated: 
4,8,9,13,14,15,16,24,25,26,27,28,29,30,31,36,37,38,39,47,48,49,50,51,52,53,54,58,59,60,64,65,66,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,102,103,104,108,109,110,111,114,119,120,121,122,127,134,136,137,138,139,141,142,147,148,149,152,153,156,157,158,159,162,163,164,165,166,167,168,169,170,171,173,175,176,179,180,183,184,185,186,191,192,195,197,198,199,200,202,206,207,210,219,220,227,228,229,230,233,234,235,240,241,243,245,246,248,249,250,251,252,253,257,259,260,266,271,272,276,277,280,281,284,286,287,289,290,291,292,296,297,298,302,304,305,306,310,311,312,313,317,318,319,321,322,324,334,337,338,339,340,341,345,346,350,351,356,359,362,364,366,367,370,371,373,376,378,382,383,384,385,386,387,388,389,391,394,395,397,398,399,400,402,403,405,406,407,409,410,411,415,416,418,419,425,431,432,433,434,435,440,441,443,445,447,449,450,452,454,455,456,461,464,466,470,472,473,481,487,488,491,492,493,494,495,496,497,498,499,501,502,504,506,507,509,511,513,515,516,51 
[... truncated]
2: In qc.affy(unnormalised, ...) :
  CDF Environment name ' hgu95av2cdf ' does not match cdfname ' 
mogene10stv1cdf '
Error in plot(qc(object)) : 
  error in evaluating the argument 'x' in selecting a method for 
function 'plot'

This: /Error: NAs in foreign function call (arg 1)/
 seems to imply that:

- there's an error in the '(arg 1)'  but which (arg 1)?   
  If this refers to the arg 
/ReadAffy(widget=TRUE,cdfname="mogene10stv1cdf")/
  then that part of the command seems to complete fine and returns an 
AffyBatch object as it should

> str(rawdata)
Formal class 'AffyBatch' [package "affy"] with 10 slots
  ..@ cdfName          : chr "mogene10stv1cdf"
  ..@ nrow             : int 1050
  ..@ ncol             : int 1050
/etc/ 

- or I have NAs in the data, but doesn't point to where or whether I 
should address them.  
If this is the critical error, I'm guessing I have to choose a 
transform that removes or floor-shifts the NAs into a computational 
form?

- the Warnings:
1: In data.row.names(row.names, rowsi, i) :
  some row.names duplicated: 4,8,9,13,14,15,16,24,25,26,27,28,29, 
  <almost every intervening # omitted> 
  ,513,515,516,51 [... truncated]

Would this be related to warning 2 below?

2: In qc.affy(unnormalised, ...) :
  CDF Environment name ' hgu95av2cdf ' does not match cdfname ' 
mogene10stv1cdf '

but if so, what is the proper way to tell QCReport that I'm using a 
non-default CDF?
the help section for QCReport doesn't describe any params for telling 
it that the CDF env is not 'hgu95av2cdf' and I've tried including that 
info in the ReadAffy() fn as noted:

ie:
> QCReport(ReadAffy(widget=TRUE,cdfname="mogene10stv1"))

> sessionInfo()
R version 2.11.1 (2010-05-31) 
i486-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] tools     tcltk     stats     graphics  grDevices utils     
datasets 
[8] methods   base     

other attached packages:
 [1] makecdfenv_1.26.0     tkWidgets_1.26.0      DynDoc_1.26.0        
 [4] widgetTools_1.26.0    hgu95av2cdf_2.6.0     affydata_1.11.10     
 [7] affyQCReport_1.26.0   lattice_0.19-11       RColorBrewer_1.0-2   
[10] affyPLM_1.24.1        preprocessCore_1.10.0 xtable_1.5-6         
[13] simpleaffy_2.24.0     gcrma_2.20.0          genefilter_1.30.0    
[16] mogene10stv1cdf_2.6.2 affy_1.26.1           Biobase_2.8.0        

loaded via a namespace (and not attached):
 [1] affyio_1.16.0        annotate_1.26.1      AnnotationDbi_1.10.2
 [4] Biostrings_2.16.9    DBI_0.2-5            grid_2.11.1         
 [7] IRanges_1.6.17       RSQLite_0.9-2        splines_2.11.1      
[10] survival_2.35-8     

Thanks for your consideration.

-- 
Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine
[ZOT 2225] / 92697  949 824-0084(o), 949 285-4487(c)
MSTB=Bldg 415 (G-5 on <http://today.uci.edu/pdf/UCI_09_map_campus.pdf>
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