[BioC] missing value

[Robert Gentleman]

Hi Yisong,

Yisong Zhen wrote:
> Dear Bioconductors,
> 
> I tried to get the quality control report generated by affyQCReport. But I
> failed.
> 
> This is my code:
> 
> library(affy);
> 
> Tucson_Array <-ReadAffy();

   There is no need to have ; at the end of lines in R.

   Could you please post the output of sessionInfo(), as asked in the 
posting guide. Then try just

  Tucson_Array

  and let us know what happens.

   And finally, let me suggest that you try the arrayQualityMetrics 
package instead of using affyQCReport. The report it generates is a bit 
more comprehensive, but currently only in HTML (I think that will change 
soon).

   best wishes
    Robert

> 
> library(affyQCReport);
> QCReport(Tucson_Array, file="TucsonQC.pdf");
> 
> This is the error message:
> 
> error density.default(newX[, i], ...) :
>         'x' contains missing values
>  Warning message:
> duplicate row.names
> 
> 12,15,20,21,22,25,26,27,31,32,33,34,38,39,40,43,44,45,48,49,50,54,55,59,60,64,65,69,70,73,74,75,78,79,83,84,88,89,90,94,95,96,97,100,101,102,106,107,108,110,111,112,114,116,117,118,119,120,121,122,125,127,131,132,135,136,139,142,143,144,146,147,148,149,151,152,154,156,158,159,160,161,162,165,167,168,171,172,173,179,180,181,182,183,184,187,190,191,196,197,198,199,205,206,207,208,211,213,217,218,219,221,222,224,227,228,230,232,234,237,238,241,242,246,249,252,253,254,255,257,259,260,263,264,266,267,269,270,271,273,275,276,279,281,283,285,288,292,294,296,298,301,304,307,309,310,312,315,316,317,321,324,326,329,332,333,334,336,339,341,343,345,346,348,351,352,353,354,357,358,360,367,369,370,372,373,375,376,378,381,383,384,385,386,388,389,391,392,394,395,397,400,403,404,405,407,410,412,415,419,421,424,426,427,429,430,432,434,436,437,439,441,443,446,449,452,454,456,457,458,461,465,468,470,471,472,474,475,477,480,483,486,490,491,493,495,498,501,504,506,507,509,510,512,513,5
> [... truncated] in: data.row.names(row.names, rowsi, i)
> 
> How can I do for next step to deal with the missing value and duplicated
> row.names? And what other packages (or steps) should I select to assess the
> within-group variation so I can discard the poor quality array (outlying
> chips)?
> 
> Thanks in advance.
> 
> Yisong
> 
> 
> 
> PS.
> 
> And here is,
> 
> sessionInfo()
> R version 2.5.0 (2007-04-23)
> i686-redhat-linux-gnu
> 
> locale:
> LC_CTYPE=zh_CN.GB18030;LC_NUMERIC=C;LC_TIME=zh_CN.GB18030;LC_COLLATE=zh_CN.GB18030;LC_MONETARY=zh_CN.GB18030;LC_MESSAGES=zh_CN.GB18030;LC_PAPER=zh_CN.GB18030;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.GB18030;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "methods"   "base"
> 
> other attached packages:
> cint06a520380fcdf              affy            affyio           Biobase
>          "1.14.0"          "1.14.2"           "1.4.1"          "1.14.1
> 
> 	[[alternative HTML version deleted]]
> 
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> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org