protocolData in quantify_MSnExp are always dropped

[sgibb]

While looking through the code to fix #264 I found the following:

MSnbase/R/quantitation-MS2-isobaric.R

Lines 69 to 76 in edcf4bd

	## Updating protocol slot
	if (nrow(protocolData(object)) > 0) {
	if (nrow(protocolData(object)) == length(reporters)) {
	.protocolData <- protocolData(object)
	} else {
	warning("protocolData does not match with reporters. Dropping it.")
	}
	}

As far as I understand the protocolData are always dropped? I suppose that should not be the case.

[lgatto]

No, I don't think it's always dropped. It is only of its dimensions don't match any more. For example if one starts with one raw files, there's a protocolData slot documenting one sample/file, but then quantifies with iTRAQ4-plex, which produces quantitation data for 4 samples. In such a case, the protocolData will only be retrained if it had 4 rows.

To be honest, I don't think this slot is used much.

[sgibb]

If the dimensions match protocolData are assigned to .protocolData. But .protocolData is never used, so in fact the information is lost.

To be honest, I don't think this slot is used much.

Me, neither.

[lgatto]

Indeed, something like this is missing

msnset@protocolData <- .protocolData

Thank you for spotting! Feel free to send a PR, or I can quickly do it.

[lgatto]

Thank you.