Question: How To Identify Quantile Normalized Expression Data
2
gravatar for jack
6.0 years ago by
jack450
jack450 wrote:

Hi,

I have miRNA microarray expression data. it's claimed that it's quantile normalized , but I'm are not sure about it. is there any method to check this ?

ADD COMMENTlink modified 6.0 years ago by george.ry1.1k • written 6.0 years ago by jack450
1

Do you mean as opposed to having been normalized by other methods than quantile, or as opposed to having been normalized at all?

ADD REPLYlink written 6.0 years ago by jobinv1.1k
4
gravatar for george.ry
6.0 years ago by
george.ry1.1k
United Kingdom
george.ry1.1k wrote:

This depends on the answer to jobinv's question in the comments on your post, but I suspect you just mean "has (any) normalization been performed?". To simply determine if a normalization procedure has been run, just dump the values and assess the data yourself:

Raw data ...

... is background corrected ...

... and then quantile normalized

You can also just assess the average expression of all probes/probesets for each array - any large deviance would suggest you're not looking at processed data.

ADD COMMENTlink written 6.0 years ago by george.ry1.1k
1

To elaborate a little: you need to generate a boxplot where x-axis = samples, y-axis = intensities. Quantile-normalized data has approximately equal medians, upper and lower quantiles.

ADD REPLYlink written 6.0 years ago by Neilfws48k

great. let's consider a case, where data is normalized, but we don't know which normalization method are used . how I can detect it ?

ADD REPLYlink written 6.0 years ago by jack450
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