## load R package
library(msDiaLogue)
## preprocessing
fileName <- "../inst/extdata/Toy_Spectronaut_Data.csv"
dataSet <- preprocessing(fileName,
filterNaN = TRUE, filterUnique = 2,
replaceBlank = TRUE, saveRm = TRUE)
## transformation
dataTran <- transform(dataSet, logFold = 2)
## annotation-based filtering
dataFiltAnno <- filterOutIn(dataTran, listName = "ALBU_BOVIN",
removeList = TRUE, saveRm = TRUE)
## normalization
dataNorm <- normalize(dataFiltAnno, normalizeType = "median")Preliminary
Examples
Before imputing missing (NA) values, proteins can be filtered based on the proportion of non-missing observations using filterNA().
The minProp argument sets the minimum required non-missing proportion for a protein to be retained, and the by argument determines whether this proportion is evaluated within each condition (by = "cond") or across all samples (by = "all").
For example, setting minProp = 0.51 and by = "cond" requires that a protein must be observed in at least 51% of replicates within each condition. If a protein fails to meet the threshold in any condition, it will be removed. And saveRm = TRUE indicates that the filtered data will be saved as a .csv file named filtered_NA_data.csv in the current working directory.
dataFilt <- filterNA(dataNorm, minProp = 0.51, by = "cond", saveRm = TRUE)| R.Condition | R.Replicate | NUD4B_HUMAN (+1) | A0A7P0T808_HUMAN (+1) | A0A8I5KU53_HUMAN (+1) | ZN840_HUMAN | CC85C_HUMAN | C9JEV0_HUMAN (+1) | C9JNU9_HUMAN | CYC_BOVIN | TRFE_BOVIN | F8W0H2_HUMAN | H0Y7V7_HUMAN (+1) | H0YD14_HUMAN | H3BUF6_HUMAN | H7C1W4_HUMAN (+1) | H7C3M7_HUMAN | TLR3_HUMAN | LRIG2_HUMAN | RAB3D_HUMAN | ADH1_YEAST | LYSC_CHICK | BGAL_ECOLI | CYTA_HUMAN | KPCB_HUMAN | LIPL_HUMAN | CO6_HUMAN | BGAL_HUMAN | SYTC_HUMAN | CASPE_HUMAN | DCAF6_HUMAN | DALD3_HUMAN | HGNAT_HUMAN | RFFL_HUMAN | RN185_HUMAN | ZN462_HUMAN | ALKB7_HUMAN | POLK_HUMAN | ACAD8_HUMAN |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 100fmol | 1 | 0.7110886 | 1.6974365 | 1.8672903 | -1.4647051 | -1.1828195 | -2.1839064 | -2.1163940 | 3.390533 | 3.925004 | -0.7955644 | 0.5275957 | 0.3054453 | -1.5384555 | -1.563866 | 0.2786759 | -2.238805 | -0.7218126 | 0.5172853 | 4.980386 | 3.891424 | 4.645080 | -0.6444628 | 0.0000000 | -1.1003773 | -2.304353 | 2.127338 | 4.699935 | -3.1345122 | -2.193699 | 0.5966224 | 1.0753304 | -2.247059 | 0.2553331 | 0.0802151 | -2.1575204 | -2.246770 | -1.9203595 |
| 100fmol | 2 | 1.3291690 | 2.6191023 | 0.2493124 | -0.6658141 | -0.4511877 | -1.7915185 | -1.2163618 | 3.935406 | 4.461227 | -0.2469202 | 0.7448112 | 0.8368538 | -1.3356925 | -1.357357 | 0.6040186 | -1.568828 | -0.3830931 | 0.8214865 | 5.296860 | 4.200130 | 5.274795 | -0.2342312 | 0.9189694 | -0.7390658 | -2.615207 | 2.164203 | 5.273847 | -2.2260264 | -1.074713 | 0.4511319 | 1.0829802 | -2.317359 | 0.6376646 | -0.9225421 | -2.3979322 | 0.000000 | -1.4317308 |
| 100fmol | 3 | 0.4784339 | 2.2448068 | 1.1199920 | -2.0149419 | -0.8627000 | -3.1172331 | -1.0047353 | 3.104257 | 4.058083 | -0.6125153 | 0.0695863 | 0.0071198 | -1.7427644 | -2.126324 | 0.6218682 | -2.407292 | -1.7721382 | 0.3807319 | 5.021505 | 3.578761 | 4.620371 | -0.7612994 | 0.2686105 | -1.8078448 | -3.131526 | 1.874052 | 4.639424 | -3.3182372 | -1.715975 | 0.1425211 | 0.2593672 | -3.000622 | 0.8892680 | -1.2914442 | -2.7601984 | -2.469142 | -2.2558682 |
| 100fmol | 4 | 1.0695424 | 2.2061044 | 1.2396459 | -1.0910666 | -0.5499771 | -3.2366723 | -1.1506536 | 3.789528 | 4.195285 | 0.0169672 | 0.8080643 | 0.5332284 | NA | -1.892344 | -0.0006345 | -1.544881 | -0.9761583 | 0.6503640 | 4.969877 | 4.052809 | 4.685813 | -0.9551142 | 0.7754941 | -1.1961556 | -2.503414 | 2.297533 | 4.940889 | -3.3253722 | -1.637636 | -0.7734746 | 0.9995338 | -3.181040 | 0.1210060 | -1.1082717 | -2.4850279 | -2.304152 | -1.7864377 |
| 200fmol | 1 | 1.2374451 | 2.7597767 | 1.5223831 | -1.0458613 | -2.1179882 | -2.3004893 | NA | 4.904306 | 4.866936 | -0.3222491 | 0.8683913 | 0.6935989 | -1.2434857 | -1.125694 | 1.1592071 | -1.436832 | -1.0569094 | 0.6455738 | 6.162104 | 5.166465 | 6.004221 | -0.6358849 | 1.2291929 | -0.5202384 | -2.348306 | 2.404777 | 5.359378 | -2.8684507 | -1.660118 | 0.6409212 | 1.5345147 | -2.176700 | -0.8247065 | -0.5620090 | -1.4195158 | -2.092036 | -0.5999810 |
| 200fmol | 2 | 1.0835077 | 2.5061290 | 1.5437753 | NA | -0.6451406 | -2.2891161 | -1.4490356 | 4.602911 | 4.780947 | -0.1192622 | 0.5369436 | NA | -1.1033534 | -1.347294 | 0.5904082 | -2.069211 | -0.7825705 | 0.7998727 | 6.035927 | 4.858498 | 6.077079 | -0.1157688 | 0.7494304 | -0.6849393 | -2.373287 | 2.218135 | 5.298451 | -3.4430880 | -1.495177 | 0.6330298 | -0.0504002 | -2.547260 | 0.0504002 | -0.8831795 | -2.2754926 | -2.169899 | -2.5736366 |
| 200fmol | 3 | 1.1895154 | -0.7610814 | 1.4827675 | -0.8782181 | -0.2278802 | -2.6460631 | -0.4371524 | 4.602658 | 5.324737 | -0.0945005 | 1.1912667 | 0.9555801 | -1.2270376 | -1.805385 | 0.6127170 | -2.003841 | -0.2808755 | 0.6251033 | 6.177903 | 5.332350 | 6.077462 | -0.6677980 | 0.5516635 | -0.8818061 | -2.631290 | 2.405737 | 5.368524 | -3.4036282 | -2.442303 | 0.8779300 | 1.5244318 | -2.543026 | 0.3252309 | -0.2958292 | -1.0326304 | -2.281109 | -2.0634390 |
| 200fmol | 4 | 1.3414509 | -0.7141775 | 2.1097733 | -0.5132050 | -0.8907703 | -2.5064949 | -0.7084750 | 5.104710 | 4.936069 | 0.0185604 | 0.6527368 | 1.2622077 | -0.7415416 | -2.490006 | 0.9681441 | -1.818448 | NA | 1.0922337 | 6.831663 | 5.361835 | 6.256076 | -0.0211462 | 1.0564532 | -0.8429453 | -2.350769 | 2.858331 | 5.788169 | -3.3014491 | -1.301171 | 0.6632118 | 1.6762101 | -2.053225 | 0.1098565 | -0.2265231 | -1.4185097 | -1.715035 | -0.4337676 |
| 50fmol | 1 | 1.1006904 | 0.0128438 | -1.6818749 | -1.3067518 | -0.7490562 | 0.2825328 | -1.5975565 | 3.812621 | 4.337253 | -0.0128438 | 0.6400481 | 1.2359921 | -1.0547978 | -1.679806 | 0.0489373 | -1.896376 | -0.8121651 | 1.0352351 | 4.910162 | 3.725298 | 4.783498 | 2.2656960 | 1.0479490 | -1.0774637 | -1.972683 | 2.784651 | 5.295658 | 0.4053746 | -2.197920 | NA | -0.3212160 | -2.701866 | -0.5696866 | -3.6395447 | -1.4537604 | -4.659186 | -1.9331960 |
| 50fmol | 2 | 1.5961351 | NA | 1.5598933 | -0.4403285 | -0.4868333 | -0.9743640 | -0.4967305 | 3.965407 | 4.704723 | 0.1790180 | 0.0539524 | 0.9962309 | -0.7435314 | -1.952132 | 0.9180740 | -1.739766 | -0.5142051 | 1.3431911 | 5.038411 | 3.933687 | 5.021220 | 0.6437576 | NA | -0.3051809 | -1.452492 | 3.208565 | 5.677698 | -1.1063367 | -1.668382 | -0.7162235 | 1.3191634 | -2.135900 | 0.4473614 | 0.0000000 | -1.8044113 | -2.489725 | -2.3514462 |
| 50fmol | 3 | 1.9377582 | -3.3201971 | 1.9463231 | -2.1765737 | -0.4435426 | -0.6520978 | -0.5861618 | 3.755350 | 4.947876 | 0.4559941 | NA | 1.4776452 | -0.6557229 | -2.603859 | 0.9301517 | NA | NA | 1.3669372 | 5.336210 | 3.913673 | 5.294049 | 1.4423886 | 1.4440220 | -0.3495777 | -1.969386 | 3.203846 | 5.970880 | -1.0907178 | -1.818956 | -0.5219278 | 1.0772742 | -2.176159 | 0.2540670 | -0.3787774 | -0.3780465 | -1.704975 | -2.6241451 |
| 50fmol | 4 | 1.3727502 | 0.6804921 | 1.1415255 | -0.8947602 | -1.1117833 | -1.7312115 | -0.5159772 | 3.571163 | 4.404044 | NA | 0.2248967 | 1.2113819 | -0.5418374 | -4.284571 | 0.6442855 | -1.781268 | -1.1704237 | 1.1056057 | 5.000695 | 3.593565 | 4.840452 | 0.5947847 | 1.2220923 | NA | NA | 2.850284 | 5.785555 | -1.2210747 | -1.299660 | 0.0000000 | 0.8876834 | -4.067901 | -0.0686141 | -0.1821314 | -1.5731591 | -1.983371 | -2.0406905 |
Note: There is no rule in the field of proteomics for filtering based on percentage of missingness, similar to there being no rule for the number of replicates required to draw a conclusion. However, reproducible observations make conclusions more credible. Setting the
minProp to 0.51 requires that any protein be observed in a majority of the replicates by condition in order to be considered. For 3 replicates, this would require 2 measurements to allow imputation of the 3rd value. If only 1 measurement is seen, the other values will remain NA, and will be filtered out in a subsequent step.