Question

Use arrayQualityMetrics package normalized cel file the number of samples has been reduced

0

Entering edit mode

shenyao3508 • 0

@shenyao3508-21891

Last seen 5.3 years ago

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.

normalization arrayQualityMetrics • 715 views

ADD COMMENT • link updated 5.3 years ago by James W. MacDonald 67k • written 5.3 years ago by shenyao3508 • 0

0

Entering edit mode

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 REPLY • link 5.3 years ago Mike Smith ★ 6.6k