## 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 100pmol | 1 | 0.6578963 | 1.6912275 | 1.523093 | -1.6229297 | -0.9854966 | -2.2020970 | -2.0487396 | 3.452154 | 3.943761 | -0.6386260 | 0.4190686 | 0.3832438 | -1.8057427 | -1.711792 | 0.2348458 | -2.451893 | -0.9267417 | 0.3315355 | 4.814073 | 3.813956 | 4.602821 | -0.6759724 | 0.0138251 | -1.1567811 | -2.703667 | 1.866666 | 4.775565 | -3.1627881 | -2.212775 | 0.3976973 | 1.0009580 | -2.370005 | 0.1730515 | 0.0000000 | -2.4413680 | -2.300598 | -2.2255399 |
| 100pmol | 2 | 1.1618220 | 2.6069381 | 0.499450 | -0.8939165 | -0.4318767 | -2.0224822 | -1.2582828 | 3.826245 | 4.398260 | -0.3855094 | 0.5688423 | 0.7856583 | -1.4665636 | -1.598602 | 0.4582302 | -1.817571 | -0.6094305 | 0.6593645 | 5.179413 | 4.207712 | 4.995489 | -0.2306371 | 0.5203989 | -1.0431798 | -2.550131 | 2.183688 | 5.153782 | -2.2734413 | -1.107578 | 0.5054164 | 1.0064713 | -2.287126 | 0.7952927 | -0.9506921 | -2.6135205 | 0.000000 | -1.6024466 |
| 100pmol | 3 | 0.6700794 | 2.3944773 | 1.292374 | -1.6925457 | -0.6687828 | -2.9987418 | -0.8270544 | 3.584108 | 4.078495 | -0.5356376 | 0.4615256 | 0.0895033 | -1.5213077 | -1.715882 | 1.0240181 | -2.147069 | -1.3776219 | 0.4651160 | 4.902153 | 3.948069 | 4.690354 | -0.6886192 | 0.4043134 | -1.4787373 | -2.907444 | 1.976459 | 4.876785 | -3.2755551 | -1.478305 | 0.1742765 | 0.5943610 | -2.635191 | 0.6053144 | -1.0476748 | -2.6195940 | -2.377350 | -2.0024438 |
| 100pmol | 4 | 0.8459180 | 2.0861542 | 1.194119 | -1.2273728 | -0.6919248 | -3.4192914 | -1.4298346 | 3.588195 | 4.071733 | -0.0242533 | 0.3495332 | 0.2761703 | NA | -1.974565 | 0.0000000 | -1.904616 | -1.1083001 | 0.4016035 | 4.859260 | 3.951123 | 4.629191 | -1.0397232 | 0.3669244 | -1.3587551 | -2.708964 | 1.949330 | 4.844947 | -3.3525778 | -2.049782 | -0.8802224 | 0.9334560 | -3.173078 | 0.1359572 | -1.1958590 | -2.7445785 | -2.634663 | -2.0589152 |
| 200pmol | 1 | 1.2367495 | 2.7209140 | 1.643059 | -0.9241627 | -2.0376118 | -2.1284865 | NA | 4.926798 | 5.071045 | -0.3843617 | 0.9573775 | 0.7511402 | -1.2486171 | -1.348386 | 1.1799089 | -1.519906 | -1.0325902 | 0.8746494 | 6.245210 | 5.245063 | 6.005343 | -0.8155394 | 0.9062960 | -0.7355826 | -2.086968 | 2.468791 | 5.354433 | -2.9824358 | -1.791057 | 0.5501207 | 1.7437348 | -2.291354 | -0.7523574 | -0.5793031 | -1.4223468 | -2.145883 | -0.5956163 |
| 200pmol | 2 | 0.8920522 | 2.1320303 | 1.448951 | NA | -0.5354481 | -2.5546421 | -1.4310495 | 4.653112 | 4.847591 | -0.2522428 | 0.4211597 | NA | -1.4825147 | -1.620216 | 0.3960272 | -2.067634 | -0.8169825 | 0.6131741 | 5.965971 | 4.954881 | 5.748865 | -0.3324563 | 0.6299749 | -0.9458767 | -2.553825 | 2.208374 | 5.114606 | -3.5195148 | -1.671696 | 0.3551539 | -0.1366535 | -2.779264 | 0.1366535 | -0.8642755 | -2.5798709 | -2.309546 | -2.3627650 |
| 200pmol | 3 | 1.2852038 | -0.8407850 | 1.836982 | -0.7498530 | -0.1779857 | -2.6275134 | -0.4297874 | 5.025134 | 5.020476 | -0.1217261 | 1.1101593 | 0.9043385 | -1.1300491 | -1.793222 | 0.8158324 | -1.870606 | -0.5628205 | 0.9300210 | 6.311564 | 5.279995 | 6.070587 | -0.5160321 | 0.7621903 | -0.8359278 | -2.306285 | 2.467474 | 5.407801 | -3.3621142 | -2.223375 | 0.8759602 | 1.3922679 | -2.542126 | 0.5557834 | -0.1662571 | -1.0158409 | -2.121038 | -1.6854347 |
| 200pmol | 4 | 1.5207481 | -0.6040897 | 2.060276 | -0.3758423 | -0.8639327 | -2.4855064 | -0.7430913 | 5.224020 | 5.377023 | 0.0161123 | 0.7924755 | 1.0651086 | -0.7232350 | -2.448600 | 0.8442237 | -1.693849 | NA | 1.1502570 | 6.655618 | 5.628997 | 6.343191 | -0.0161123 | 1.0727957 | -0.6382337 | -2.135701 | 2.815138 | 5.691298 | -2.9208223 | -1.419815 | 0.9018856 | 1.6702296 | -2.088800 | 0.1983234 | -0.0738239 | -1.3827316 | -1.718714 | -0.5015723 |
| 50pmol | 1 | 1.3569066 | -0.0418239 | -1.605374 | -1.1289594 | -0.9034872 | 0.0539109 | -1.5868197 | 3.547765 | 4.397999 | 0.0418239 | 0.6383018 | 1.0090953 | -0.9876086 | -1.713483 | 0.1019217 | -1.921549 | -0.9836494 | 1.0378691 | 4.827457 | 3.633069 | 4.671661 | 2.3687002 | 0.8333762 | -1.0023667 | -2.155108 | 2.618091 | 5.473048 | 0.5514687 | -1.981854 | NA | -0.3248609 | -2.734260 | -0.6292096 | -3.5325733 | -1.2902634 | -4.787183 | -2.0214147 |
| 50pmol | 2 | 1.6024612 | NA | 1.579083 | -0.5872764 | -0.4786125 | -0.9419543 | -0.6649410 | 3.779592 | 4.677255 | 0.2521855 | 0.1196002 | 1.1937745 | -0.7693976 | -2.240260 | 0.7951258 | -1.798939 | -0.4338096 | 1.3649676 | 5.070432 | 3.993905 | 4.912229 | 0.8090999 | NA | -0.4372525 | -1.552151 | 2.850557 | 5.750686 | -1.2356313 | -1.562935 | -0.8838660 | 1.2757206 | -2.381622 | 0.6504456 | 0.0000000 | -1.7357928 | -2.468666 | -2.2680179 |
| 50pmol | 3 | 1.6576732 | -3.4526216 | 1.552080 | -2.4702967 | -0.6505471 | -0.8524562 | -0.7371056 | 3.729220 | 4.679342 | 0.2920380 | NA | 1.1969443 | -0.6623836 | -2.395087 | 0.6664780 | NA | NA | 1.3371078 | 5.157961 | 3.997182 | 4.927047 | 0.9774672 | 1.0924818 | -0.5422253 | -1.947256 | 2.893225 | 5.804690 | -1.1925628 | -1.811837 | -0.6752742 | 1.0031749 | -2.315473 | 0.2331366 | -0.8188381 | -0.5723308 | -2.056650 | -2.4453921 |
| 50pmol | 4 | 1.3361532 | 0.6443309 | 1.275179 | -1.1057418 | -1.2905885 | -1.5849506 | -0.6332468 | 3.345342 | 4.341111 | NA | 0.0000000 | 1.1344349 | -0.8056352 | -4.298759 | 0.5579245 | -2.058139 | -1.0248051 | 0.9560929 | 4.778818 | 3.668827 | 4.637064 | 0.5802164 | 0.9408524 | NA | NA | 2.591638 | 5.452341 | -1.6387928 | -1.429612 | 0.1904210 | 0.7490866 | -4.231605 | -0.1802510 | -0.3981666 | -1.8530176 | -2.042691 | -2.1323101 |
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.