2 votes

To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?

There is no direct support for this by best knowledge. Similar questions have been asked previously in the Bioconductor support forum, for example: https://support.bioconductor.org/p/64300/#64793 They ...
ATpoint's user avatar
  • 948
1 vote

Non-parametric, background-based tests on proteomics data from Proteome Discoverer v2.5?

Small samples size and parametric tests are not mutually exclusive. Specialized software has been developed to leverage sharing information across measurements to boost power, that is called ...
xz99890's user avatar
  • 11
1 vote

Reduce Overfit by removing insignificant proteins through PSEA analysis

Overfitting is usually resolved by adding more data and not removing data sets. The technical blurb is 'augmenting' your training data set to revolve overfitting. It is possible there is a very large ...
M__'s user avatar
  • 11.3k
1 vote

Heat map of protein expression from normalized abundance

The -2 to 2 should be the normalized version of log2 data (maybe mean or median normalization). This is commonly used in heatmaps to show downregulated value vs. upregulated value.
Pete Kittinun's user avatar

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