dataProcess.RdProcess MS data: clean, normalize and summarize before differential analysis
dataProcess( raw, logTrans = 2, normalization = "equalizeMedians", nameStandards = NULL, featureSubset = "all", remove_uninformative_feature_outlier = FALSE, min_feature_count = 2, n_top_feature = 3, summaryMethod = "TMP", equalFeatureVar = TRUE, censoredInt = "NA", MBimpute = TRUE, remove50missing = FALSE, fix_missing = NULL, maxQuantileforCensored = 0.999, use_log_file = TRUE, append = FALSE, verbose = TRUE, log_file_path = NULL )
| raw | name of the raw (input) data set. |
|---|---|
| logTrans | base of logarithm transformation: 2 (default) or 10. |
| normalization | normalization to remove systematic bias between MS runs. There are three different normalizations supported: 'equalizeMedians' (default) represents constant normalization (equalizing the medians) based on reference signals is performed. 'quantile' represents quantile normalization based on reference signals 'globalStandards' represents normalization with global standards proteins. If FALSE, no normalization is performed. |
| nameStandards | optional vector of global standard peptide names. Required only for normalization with global standard peptides. |
| featureSubset | "all" (default) uses all features that the data set has. "top3" uses top 3 features which have highest average of log-intensity across runs. "topN" uses top N features which has highest average of log-intensity across runs. It needs the input for n_top_feature option. "highQuality" flags uninformative feature and outliers. |
| remove_uninformative_feature_outlier | optional. Only required if featureSubset = "highQuality". TRUE allows to remove 1) noisy features (flagged in the column feature_quality with "Uninformative"), 2) outliers (flagged in the column, is_outlier with TRUE, before run-level summarization. FALSE (default) uses all features and intensities for run-level summarization. |
| min_feature_count | optional. Only required if featureSubset = "highQuality". Defines a minimum number of informative features a protein needs to be considered in the feature selection algorithm. |
| n_top_feature | optional. Only required if featureSubset = 'topN'. It that case, it specifies number of top features that will be used. Default is 3, which means to use top 3 features. |
| summaryMethod | "TMP" (default) means Tukey's median polish, which is robust estimation method. "linear" uses linear mixed model. |
| equalFeatureVar | only for summaryMethod = "linear". default is TRUE. Logical variable for whether the model should account for heterogeneous variation among intensities from different features. Default is TRUE, which assume equal variance among intensities from features. FALSE means that we cannot assume equal variance among intensities from features, then we will account for heterogeneous variation from different features. |
| censoredInt | Missing values are censored or at random. 'NA' (default) assumes that all 'NA's in 'Intensity' column are censored. '0' uses zero intensities as censored intensity. In this case, NA intensities are missing at random. The output from Skyline should use '0'. Null assumes that all NA intensites are randomly missing. |
| MBimpute | only for summaryMethod = "TMP" and censoredInt = 'NA' or '0'. TRUE (default) imputes 'NA' or '0' (depending on censoredInt option) by Accelated failure model. FALSE uses the values assigned by cutoffCensored. |
| remove50missing | only for summaryMethod = "TMP". TRUE removes the runs which have more than 50% missing values. FALSE is default. |
| fix_missing | Optional, same as the `fix_missing` parameter in MSstatsConvert::MSstatsBalancedDesign function |
| maxQuantileforCensored | Maximum quantile for deciding censored missing values, default is 0.999 |
| use_log_file | logical. If TRUE, information about data processing will be saved to a file. |
| append | logical. If TRUE, information about data processing will be added to an existing log file. |
| verbose | logical. If TRUE, information about data processing wil be printed to the console. |
| log_file_path | character. Path to a file to which information about data processing will be saved. If not provided, such a file will be created automatically. If `append = TRUE`, has to be a valid path to a file. |
# Consider a raw data (i.e. SRMRawData) for a label-based SRM experiment from a yeast study # with ten time points (T1-T10) of interests and three biological replicates. # It is a time course experiment. The goal is to detect protein abundance changes # across time points. head(SRMRawData)#> ProteinName PeptideSequence PrecursorCharge FragmentIon ProductCharge #> 243 IDHC ATDVIVPEEGELR 2 y7 NA #> 244 IDHC ATDVIVPEEGELR 2 y7 NA #> 245 IDHC ATDVIVPEEGELR 2 y8 NA #> 246 IDHC ATDVIVPEEGELR 2 y8 NA #> 247 IDHC ATDVIVPEEGELR 2 y9 NA #> 248 IDHC ATDVIVPEEGELR 2 y9 NA #> IsotopeLabelType Condition BioReplicate Run Intensity #> 243 H 1 ReplA 1 84361.08350 #> 244 L 1 ReplA 1 215.13526 #> 245 H 1 ReplA 1 29778.10188 #> 246 L 1 ReplA 1 98.02134 #> 247 H 1 ReplA 1 17921.29255 #> 248 L 1 ReplA 1 60.47029# Log2 transformation and normalization are applied (default) QuantData<-dataProcess(SRMRawData, use_log_file = FALSE)#> INFO [2021-07-05 20:05:33] ** Features with one or two measurements across runs are removed. #> INFO [2021-07-05 20:05:33] ** Fractionation handled. #> INFO [2021-07-05 20:05:33] ** Updated quantification data to make balanced design. Missing values are marked by NA #> INFO [2021-07-05 20:05:33] ** Log2 intensities under cutoff = 3.776 were considered as censored missing values. #> INFO [2021-07-05 20:05:33] ** Log2 intensities = NA were considered as censored missing values. #> INFO [2021-07-05 20:05:33] ** Use all features that the dataset originally has. #> INFO [2021-07-05 20:05:33] #> # proteins: 2 #> # peptides per protein: 2-2 #> # features per peptide: 3-3 #> INFO [2021-07-05 20:05:33] #> 1 2 3 4 5 6 7 8 9 10 #> # runs 3 3 3 3 3 3 3 3 3 3 #> # bioreplicates 3 3 3 3 3 3 3 3 3 3 #> # tech. replicates 1 1 1 1 1 1 1 1 1 1 #> INFO [2021-07-05 20:05:33] == Start the summarization per subplot... #> | | | 0% | |=================================== | 50% | |======================================================================| 100% #> INFO [2021-07-05 20:05:33] == Summarization is done.#> PROTEIN PEPTIDE TRANSITION FEATURE LABEL GROUP RUN #> 1 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA H 0 1 #> 2 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA L 1 1 #> 3 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA H 0 2 #> 4 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA L 1 2 #> 5 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA H 0 3 #> 6 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA L 1 3 #> SUBJECT FRACTION originalRUN censored INTENSITY ABUNDANCE newABUNDANCE #> 1 0 1 1 FALSE 84361.0835 15.855859 15.855859 #> 2 1 1 1 FALSE 215.1353 7.240669 7.240669 #> 3 0 1 2 FALSE 62109.5876 15.801179 15.801179 #> 4 2 1 2 FALSE 1205.2252 10.113738 10.113738 #> 5 0 1 3 FALSE 65114.3646 15.755022 15.755022 #> 6 3 1 3 FALSE 1476.3046 10.292109 10.292109 #> predicted #> 1 NA #> 2 NA #> 3 NA #> 4 NA #> 5 NA #> 6 NA# Log10 transformation and normalization are applied QuantData1<-dataProcess(SRMRawData, logTrans=10, use_log_file = FALSE)#> INFO [2021-07-05 20:05:33] ** Features with one or two measurements across runs are removed. #> INFO [2021-07-05 20:05:33] ** Fractionation handled. #> INFO [2021-07-05 20:05:33] ** Updated quantification data to make balanced design. Missing values are marked by NA #> INFO [2021-07-05 20:05:33] ** Log2 intensities under cutoff = 1.1367 were considered as censored missing values. #> INFO [2021-07-05 20:05:33] ** Log2 intensities = NA were considered as censored missing values. #> INFO [2021-07-05 20:05:33] ** Use all features that the dataset originally has. #> INFO [2021-07-05 20:05:33] #> # proteins: 2 #> # peptides per protein: 2-2 #> # features per peptide: 3-3 #> INFO [2021-07-05 20:05:33] #> 1 2 3 4 5 6 7 8 9 10 #> # runs 3 3 3 3 3 3 3 3 3 3 #> # bioreplicates 3 3 3 3 3 3 3 3 3 3 #> # tech. replicates 1 1 1 1 1 1 1 1 1 1 #> INFO [2021-07-05 20:05:33] == Start the summarization per subplot... #> | | | 0% | |=================================== | 50% | |======================================================================| 100% #> INFO [2021-07-05 20:05:33] == Summarization is done.#> PROTEIN PEPTIDE TRANSITION FEATURE LABEL GROUP RUN #> 1 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA H 0 1 #> 2 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA L 1 1 #> 3 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA H 0 2 #> 4 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA L 1 2 #> 5 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA H 0 3 #> 6 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA L 1 3 #> SUBJECT FRACTION originalRUN censored INTENSITY ABUNDANCE newABUNDANCE #> 1 0 1 1 FALSE 84361.0835 4.773089 4.773089 #> 2 1 1 1 FALSE 215.1353 2.179659 2.179659 #> 3 0 1 2 FALSE 62109.5876 4.756629 4.756629 #> 4 2 1 2 FALSE 1205.2252 3.044538 3.044538 #> 5 0 1 3 FALSE 65114.3646 4.742734 4.742734 #> 6 3 1 3 FALSE 1476.3046 3.098233 3.098233 #> predicted #> 1 NA #> 2 NA #> 3 NA #> 4 NA #> 5 NA #> 6 NA# Log2 transformation and no normalization are applied QuantData2<-dataProcess(SRMRawData,normalization=FALSE, use_log_file = FALSE)#> INFO [2021-07-05 20:05:33] ** Features with one or two measurements across runs are removed. #> INFO [2021-07-05 20:05:33] ** Fractionation handled. #> INFO [2021-07-05 20:05:33] ** Updated quantification data to make balanced design. Missing values are marked by NA #> INFO [2021-07-05 20:05:34] ** Log2 intensities under cutoff = 3.7346 were considered as censored missing values. #> INFO [2021-07-05 20:05:34] ** Log2 intensities = NA were considered as censored missing values. #> INFO [2021-07-05 20:05:34] ** Use all features that the dataset originally has. #> INFO [2021-07-05 20:05:34] #> # proteins: 2 #> # peptides per protein: 2-2 #> # features per peptide: 3-3 #> INFO [2021-07-05 20:05:34] #> 1 2 3 4 5 6 7 8 9 10 #> # runs 3 3 3 3 3 3 3 3 3 3 #> # bioreplicates 3 3 3 3 3 3 3 3 3 3 #> # tech. replicates 1 1 1 1 1 1 1 1 1 1 #> INFO [2021-07-05 20:05:34] == Start the summarization per subplot... #> | | | 0% | |=================================== | 50% | |======================================================================| 100% #> INFO [2021-07-05 20:05:34] == Summarization is done.#> PROTEIN PEPTIDE TRANSITION FEATURE LABEL GROUP RUN #> 1 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA H 0 1 #> 2 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA L 1 1 #> 3 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA H 0 2 #> 4 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA L 1 2 #> 5 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA H 0 3 #> 6 IDHC ATDVIVPEEGELR_2 y7_NA ATDVIVPEEGELR_2_y7_NA L 1 3 #> SUBJECT FRACTION originalRUN censored INTENSITY ABUNDANCE newABUNDANCE #> 1 0 1 1 FALSE 84361.0835 16.36429 16.36429 #> 2 1 1 1 FALSE 215.1353 7.74910 7.74910 #> 3 0 1 2 FALSE 62109.5876 15.92253 15.92253 #> 4 2 1 2 FALSE 1205.2252 10.23509 10.23509 #> 5 0 1 3 FALSE 65114.3646 15.99069 15.99069 #> 6 3 1 3 FALSE 1476.3046 10.52777 10.52777 #> predicted #> 1 NA #> 2 NA #> 3 NA #> 4 NA #> 5 NA #> 6 NA