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Bug fix to release #85

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Nov 14, 2024
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2 changes: 1 addition & 1 deletion R/groupComparisonTMT.R
Original file line number Diff line number Diff line change
Expand Up @@ -256,7 +256,7 @@ MSstatsModerateTTest = function(summarized, fitted_models, moderated) {
eb_input_df = fitted_models[variance_df != 0 & !is.na(variance_df),
variance_df]
if (moderated) {
eb_fit = limma::squeezeVar(eb_input_s2, eb_input_df)
eb_fit = limma::squeezeVar(eb_input_s2, eb_input_df, legacy = TRUE)
df_prior = eb_fit$df.prior
variance_prior = eb_fit$var.prior
} else { ## ordinary t statistic
Expand Down
7 changes: 6 additions & 1 deletion inst/NEWS.Rd
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,11 @@
\title{MSstatsTMT News}
\encoding{UTF-8}

\section{Changes in version 2.14.1 (2024-10-30) }{\itemize{
\item Added interactive plotting functions using Plotly.
\item Integrated support for ProteinProspector data conversion via MSstatsConvert.
}}

\section{Changes in version 2.6.1 (2023-02-26) }{\itemize{
\item Minor change: update PhilosophertoMSstatsTMTFormat function
normalization
Expand Down Expand Up @@ -116,4 +121,4 @@ condition and BioReplicate columns.
}}
\section{Changes in version 1.0.0 (2018-09-21)}{\itemize{
\item Submitted to Bioconductor
}}
}}
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