[BioC] quality control of affy Chips for miRNA

[James W. MacDonald]

Hi Assa,

On 2/28/2011 4:30 AM, Assa Yeroslaviz wrote:
> 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.

Not sure what you mean here. Do you in fact mean that you used 
biocLite() to get the correct cdf package for this chip? Which is what 
you should be saying. There is almost never a reason for you to be 
getting the 'raw' cdf from Affy.

> 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.

Right. Which means you should read the package vignette, where they give 
some indication what to do to specify QC parameters. Did you?

This does raise a bit of a problem, as I don't see any actin or GAPDH 
probes on this chip. Perhaps you can get away with just specifying 
something for the spike-in controls. Or maybe not. You will have to try 
and see what happens.


> 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 don't know of any miRNA-specific qc packages. But many of the 
functions in simpleaffy, AffyQCReport, and arrayQualityMetrics should 
work. However, you might need to pick and choose what to run rather than 
simply running the main wrapper function, as many of the functions are 
likely not to work for this chip.

Best,

Jim


>
> 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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>
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-- 
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
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