Hi BioC users,

I'm working on a set of affy chips for miRNA. I would like to run some
quality control tests but none of the functions I am trying seems to work.
I have tried the AffyQCReport, affycoretools and simpleaffy. But every time
I am getting the error message that my qcdef file is not there.
I downloaded the files from affymetrix and rename the miRNA-1_0_2Xgain.CDF
into mirna102xgaincdf.
than I did
> setQCEnvironment("mirna102xgaincdf", path=getwd())

which apperently works just fine, but:
> QCReport(rawData)
Error in setQCEnvironment(cdfn) :
  Could not find array definition file ' mirna102xgaincdf.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.
In addition: Warning message:
In data.row.names(row.names, rowsi, i) :
  some row.names duplicated:
3,4,8,9,10,14,15,16,20,21,22,23,28,29,30,31,35,36,37,38,43,44,45,49,50,51,52,56,57,58,62,63,64,68,69,70,75,76,77,81,82,83,84,88,89,90,94,95,96,97,101,102,103,107,
108,109,113,114,115,120,121,122,126,127,128,132,133,134,135,139,140,141,145,146,147,152,153,154,158,159,160,164,165,166,167,172,173,174,196,197,198,199,200,201,207,208,209,210,211,217,
218,219,220,221,227,228,229,230,231,237,238,239,240,241,245,246,247,253,254,255,256,257,258,264,265,266,267,268,274,275,276,277,278,284,285,286,287,288,294,295,296,297,298,304,305,306,
307,308,314,315,316,317,318,324,325,326,327,328,335,336,337,338,339,345,346,347,348,349,355,356,357,358,359,365,366,367,368,369,375,376,377,378,379,385,386,387,388,389,396,397,398,399,
400,404,405,406,407,413,414,415,416,417,424,425,426,427,428,434,435,436,437,438,444,445,446,447,448,454,455,456,457,458,464,465,466,467,468,474,475,476,477,478,485,486,487,488,489,495,
496,497,498,499,505,506,507,508,509,515,516,517,518,519,525,526,527,528,529
[... truncated]

I would like to know whether there are some specific qc tools or R-packages
for the miRNA from Affymetrix (the older version of the arrays).

I did an MA plot of the arrays and they looks fine to me, but I would still
like to sun some more tests.

THX,
Assa

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