Question: Use arrayQualityMetrics package normalized cel file the number of samples has been reduced
gravatar for shenyao3508
4 weeks ago by
shenyao35080 wrote:
dir_cels='C:\\Users\\35081\\Desktop\\新建文件夹 (2)\\51105'#设置路径变量
affy_data = ReadAffy(celfile.path=dir_cels)#读取数据
eset = mas5(affy_data)#mas5方法标准化
arrayQualityMetrics(expressionset = eset,
                    outdir = "fig",
                    force = TRUE,
                    do.logtransform = T)

I have imported 400 samples, but only 70 of them are drawn,I want to know why, thank you kindly.

ADD COMMENTlink written 4 weeks ago by shenyao35080

I think you need to provide some more details before anyone can help with this. It's always good to include the output of the command sessionInfo() so people can see the versions of R and the various packages you are using.

It would also be helpful to know if you see any error messages etc. You might also want to check that you have really imported all 400 samples by checking the dimensions of the eset object. At the moment it is hard to diagnose whether an issue lies with the data import or the report generation.

ADD REPLYlink written 4 weeks ago by Mike Smith4.0k
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