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, 108,109,113,114,115,120,121,122,126,127,128,132,133,134,135,139,140,14 1,145,146,147,152,153,154,158,159,160,164,165,166,167,172,173,174,196, 197,198,199,200,201,207,208,209,210,211,217, 218,219,220,221,227,228,229,230,231,237,238,239,240,241,245,246,247,25 3,254,255,256,257,258,264,265,266,267,268,274,275,276,277,278,284,285, 286,287,288,294,295,296,297,298,304,305,306, 307,308,314,315,316,317,318,324,325,326,327,328,335,336,337,338,339,34 5,346,347,348,349,355,356,357,358,359,365,366,367,368,369,375,376,377, 378,379,385,386,387,388,389,396,397,398,399, 400,404,405,406,407,413,414,415,416,417,424,425,426,427,428,434,435,43 6,437,438,444,445,446,447,448,454,455,456,457,458,464,465,466,467,468, 474,475,476,477,478,485,486,487,488,489,495, 496,497,498,499,505,506,507,508,509,515,516,517,518,519,525,526,527,52 8,529 [... 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 [[alternative HTML version deleted]]

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, 50,51,52,56,57,58,62,63,64,68,69,70,75,76,77,81,82,83,84,88,89,90,94,9 5,96,97,101,102,103,107, > 108,109,113,114,115,120,121,122,126,127,128,132,133,134,135,139,140, 141,145,146,147,152,153,154,158,159,160,164,165,166,167,172,173,174,19 6,197,198,199,200,201,207,208,209,210,211,217, > 218,219,220,221,227,228,229,230,231,237,238,239,240,241,245,246,247, 253,254,255,256,257,258,264,265,266,267,268,274,275,276,277,278,284,28 5,286,287,288,294,295,296,297,298,304,305,306, > 307,308,314,315,316,317,318,324,325,326,327,328,335,336,337,338,339, 345,346,347,348,349,355,356,357,358,359,365,366,367,368,369,375,376,37 7,378,379,385,386,387,388,389,396,397,398,399, > 400,404,405,406,407,413,414,415,416,417,424,425,426,427,428,434,435, 436,437,438,444,445,446,447,448,454,455,456,457,458,464,465,466,467,46 8,474,475,476,477,478,485,486,487,488,489,495, > 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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