quality: Quality Check on a Set of Spectra
In PROcess: Ciphergen SELDI-TOF Processing

Description Usage Arguments Details Value Author(s) Examples

Compute three quality parameters for a set of spectra.

1	quality(Ma, peakinfofile, cutoff)

`Ma`	a Matrix where the baseline-subtracted spectra are stored column wise.
`peakinfofile`	a ‘.csv’ file in the same format as Ciphergen's peak info file, with 5 columns data. See Details of `getPeaks`.
`cutoff`	The point in m/z below which spectra are cutoff.

The quality parameters are computed a la fashion de Mani. 1. Estimate noise by moving average with a 5 point window. 2. Estimate the noise envelop by 3 times the standard deviation of noise in a 251 point moving window. 3. Compute the area under the baseline-subtracted curve, area0. 4. Compute the area after subtracting the noise envelop from the baseline-subtracted curve, area1. 5. Parameter 'Quality' is defined as area1/area0. 6. Parameter 'Retain' is defined as the number of points with height above 5 times the noise envelop over total number of points in the spectrum. 7. Detect peaks in each spectrum by getPeaks or Ciphergen software. 8. Parameter 'peak' is defined as the number of peaks in a spectrum divided by the mean number of peaks across spectra.

A spectrum is considered to be of poor quality if Quality<0.4, Retain<0.1 and peak<0.5 simultaneously.

A matrix with three named columns, 'Quality','Retain' and 'peak', with spectrum file names as row names.

Xiaochun Li