estimateNoise of Spectrum objects

[lgatto]

@sgibb there would be some interest here to estimate signal-to-ratio using MSnbase. The MALDIquant::estimateNoise method seems to be a good candidate.

Have you ever tried it on MS2 spectra? Do the spectra need to be in profile mode, or is centroided fine too?

[sgibb]

MALDIquant::estimateNoise works on profile mode only. All noise estimators that I am aware of are metrics applied on fixed/moving windows (median/mad/quantile etc.), smoothing functions (loess, friedman' supersmoother, ...) or wavelet based methods. IHMO all these methods just work on profile data.
I am not sure whether it is possible to estimate noise in centroided MS2 spectra. What is the noise in these spectra (maybe there are some superfluous fragments?)?

[lgatto]

What is the noise in these spectra (maybe there are some superfluous fragments?)?

Yes, that's what the discussion centred around.

May be it would be worth adding the method for spectra that where centroided(x) == TRUE?

[sgibb]

On 2016-02-22 18:17:03, notifications@github.com wrote:

What is the noise in these spectra (maybe there are some superfluous fragments?)?

Yes, that's what the discussion centred around.

May be it would be worth adding the method for spectra that where centroided(x) == TRUE?
Did you mean centroided(x) == FALSE ?

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[lgatto]

Did you mean centroided(x) == FALSE ?

Yes, indeed. The problem is that it is easy to fool this, as there is a centroided replacement method.

[lgatto]

I haven't heard of this request again. But it might be useful, at some point. to add these methods for Spectrum objects where centroided is FALSE.

[sgibb]

That would be no problem. The output of MALDIquant::estimateNoise is a matrix with two columns with the estimated noise per data point
(colnames(x) == c("mz", "intensity")). Would that be enough or do you want to
store the information somewhere in the Spectrum1 object?

On 2016-03-09 18:28:34, notifications@github.com wrote:

I haven't heard of this request again. But it might be useful, at some point. to add these methods for Spectrum objects where centroided is FALSE.

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[lgatto]

There is not place to store this in Spectrum objects, so I think returning a matrix as in MALDIquant is the best solution.

[lgatto]

Thank you. One question/comment - for empty spectra, your return NA. What would you think of returning a matrix of dimension 0 by 2 with appropriate column names, to make the output of estimateNoise consistent?

[sgibb]

Good point. Changed in 5a59ce1.
On 2016-03-10 19:45:58, notifications@github.com wrote:

Thank you. One question/comment - for empty spectra, your return NA. What would you think of returning a matrix of dimension 0 by 2 with appropriate column names, to make the output of estimateNoise consistent?

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[lgatto]

I have alsoadded the estimateNoise,MSnExp method, that iterates over all spectra and returns a list of noise matrices 0038ebb.

[sgibb]

Great!
On 2016-03-11 10:48:47, notifications@github.com wrote:

I have alsoadded the estimateNoise,MSnExp method, that iterates over all spectra and returns a list of noise matrices 0038ebb.

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