[BioC] Help on PLGEM R Package Data Import

[Norman Pavelka]

Dear Qi,

Thank you for your interest in PLGEM!

I am CC'ing my reply to the Bioconductor mailing list, as this is the
best forum to address your question. I strongly recommend you to
subscribe and send further queries there. (You may always CC me to get
a more rapid response.)

Your question is about how to load your data into R/Bioconductor.
Since the object that PLGEM needs as an input is of type
'ExpressionSet', you'll have to learn how to build such an object in
R. Doing it from scratch is a bit cumbersome, but you could use
function 'readExpressionSet' from package Biobase to make your life
easier. Type the following in your R prompt to get the help page:

library(Biobase)
?readExpressionSet

For PLGEM, you will only need a single 'exprsFile' and a single 'phenoDataFile':

* The 'exprsFile' is going to be a tab-delimited text file in which
the first column contains your protein identifiers and the subsequent
columns contain NSAF values from the various MS runs you performed. Be
sure to put a meaningful header on top of each column (except for the
first column). Do not use any spaces or special characters in your
column headers, though, because it will cause some problems. For those
proteins that were not identified in all your runs, replace the
missing values with a zero.

* The 'phenoDataFile' instead is going to be a description of your
columns in your 'exprsFile', i.e. a description of your experimental
design. Note that the row names of the 'phenoDataFile' need to exactly
match the column names of the 'exprsFile'.

To make it easier, I'm attaching an example with some random numbers.
Copy these two files into your working directory and run the following
code:

library(plgem)
eset <- readExpressionSet("example-exprsFile.txt", "example-phenoDataFile.txt")
plgemResult <- run.plgem(eset)

(Of course the results are going to look aweful, because I just put in
some random numbers...)
Please direct further queries directly to the Bioconductor mailing
list. Good luck and let me know how it worked!

Cheers,
Norman

On Wed, Sep 21, 2011 at 10:37 AM, Wu Qi <qwu at dicp.ac.cn> wrote:
> Dear Norman,
>
>
>
> My name is Qi Wu, I’m a Chinese student working on quantitative proteomics,
> recently your PLGEM algorithm interested me. It seems a better choice than
> conventional t test.
>
> I’m a beginner in statistics, after installing PLGEM R package, I followed
> the instruction on “An introduction to PLGEM, Mattia Pelizzola and Norman
> Pavelka, April 13, 2011” running the wrapper mode and got the sample
> figures. But I don’t know how to import my own data. I couldn’t open the
> sample data named “LPSeset” using Excel or UltraEdit, so I had no idea how
> the data was organized. Now I could generate replicate Excel or plain text
> files containing proteins abundance values of different status, could you
> tell me how can I import such data in PLGEM R package and get a list
> containing those significantly changed proteins? I searched the internet for
> quite a long time and got nothing.
>
> Thanks very much for contributing your wonderful algorithm, your reply is
> high appreciated.
>
>
>
> Best Regards,
>
> Qi Wu
>
>
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	run1	run2	run3	run4	run5	run6
protein1	0.272105158	0.578182635	0.754035242	0.145940092	0.769239904	0.701316978
protein2	0.764643801	0.894118526	0.548281721	0.711020065	0.464191732	0.465665834
protein3	0.812542045	0.725245955	0.355091457	0.733231007	0.3719215	0.573931768
protein4	0.532098925	0.576436094	0.79932147	0.923533755	0.240087811	0.298329571
protein5	0.069322058	0.342420665	0.595869364	0.871297892	0.290066368	0.262239274
protein6	0.651908779	0.08587925	0.41497138	0.593448418	0.135282783	0.237435055
protein7	0.00676442	0.868917734	0.123948979	0.309431888	0.39153302	0.974454413
protein8	0.252936075	0.82627297	0.753852382	0.637724441	0.818835489	0.536654514
protein9	0.939906975	0.411477747	0.831390849	0.081767998	0.666160992	0.893382316
protein10	0.168850397	0.485616703	0.205180179	0.156619923	0.508252278	0.471131498
protein11	0.196314728	0.32468134	0.761186946	0.558866463	0.67901396	0.489973861
protein12	0.861746035	0.102611596	0.855005987	0.73792888	0.32983249	0.21108694
protein13	0.951873673	0.30003462	0.006940712	0.629648448	0.629938638	0.832315979
protein14	0.640402383	0.294533828	0.529832604	0.371573318	0.506894077	0.143067205
protein15	0.73583378	0.14851005	0.595233972	0.885030862	0.325172829	0.026206465
protein16	0.908470945	0.718603101	0.708392513	0.50143069	0.193894918	0.665979581
protein17	0.496500532	0.535995474	0.094783653	0.401989162	0.94661853	0.601725604
protein18	0.194425978	0.340924645	0.712342405	0.080625936	0.819505964	0.616081334
protein19	0.430001631	0.441905248	0.402944474	0.843559756	0.31844547	0.901831521
protein20	0.639123746	0.624013128	0.359589383	0.342791867	0.564777258	0.244177715
protein21	0.924487693	0.757481476	0.891131304	0.609658293	0.010763033	0.127580434
protein22	0.218318705	0.452645588	0.911919944	0.078377704	0.567760287	0.602822591
protein23	0.736702867	0.985518833	0.369754987	0.422809818	0.928399206	0.608567008
protein24	0.320451014	0.071640958	0.839071677	0.426467979	0.442474916	0.222783007
protein25	0.616781335	0.935056527	0.721135255	0.155921482	0.674421545	0.945110022
protein26	0.141025926	0.21758066	0.56221364	0.172119983	0.464236048	0.481820792
protein27	0.924781234	0.994016109	0.901588658	0.131451283	0.749907303	0.546611201
protein28	0.82062542	0.731001115	0.261704493	0.015184267	0.340863612	0.311089976
protein29	0.808924799	0.06599185	0.711024246	0.303225398	0.934253553	0.441136691
protein30	0.829397695	0.962024924	0.701677997	0.269678982	0.905625469	0.696369106
protein31	0.688649426	0.429196772	0.850694014	0.530922811	0.489442554	0.340990442
protein32	0.271072588	0.310993208	0.066286859	0.667186432	0.216603295	0.98393354
protein33	0.177641473	0.947536386	0.314142345	0.335356201	0.03103037	0.308629266
protein34	0.083279722	0.505583206	0.149014369	0.93389466	0.689173154	0.393801431
protein35	0.307865094	0.893705322	0.66594377	0.346686825	0.545788992	0.935939284
protein36	0.658938081	0.117871285	0.664053321	0.076622596	0.963525499	0.52271653
protein37	0.627671082	0.017791532	0.643219901	0.768227117	0.492449358	0.363140614
protein38	0.355743028	0.385378738	0.160308018	0.471810777	0.086925445	0.174162284
protein39	0.337959389	0.385260383	0.177478255	0.736542854	0.566532246	0.265694763
protein40	0.96810809	0.918746911	0.162265268	0.255419097	0.908330676	0.274357173
protein41	0.015773201	0.355726353	0.480739577	0.169213899	0.342018637	0.535936092
protein42	0.577332614	0.29894483	0.75724934	0.395812026	0.566983833	0.707412429
protein43	0.515129951	0.357157564	0.526637623	0.854330064	0.049939994	0.695080804
protein44	0.871384099	0.616546877	0.697200572	0.127922319	0.219454732	0.495248987
protein45	0.374477308	0.594947101	0.417492497	0.686996851	0.640584105	0.088030237
protein46	0.071587003	0.989157339	0.413504575	0.37602752	0.747968579	0.759316849
protein47	0.51427987	0.860039769	0.769387922	0.490167111	0.490964504	0.592018772
protein48	0.484559854	0.356943493	0.339023292	0.995063496	0.30532164	0.608724785
protein49	0.912141251	0.558137217	0.680421621	0.99945879	0.537633599	0.188452237
protein50	0.494583561	0.611372237	0.854799472	0.541990958	0.03840154	0.350093271
protein51	0.011361507	0.012479676	0.918867369	0.912596163	0.682556294	0.975385196
protein52	0.778622728	0.912687805	0.944790793	0.883330044	0.973987955	0.206676026
protein53	0.474411517	0.182070146	0.232991395	0.485088865	0.508959881	0.206590012
protein54	0.911200361	0.354936593	0.056552516	0.944233546	0.650099845	0.145641756
protein55	0.775455866	0.127316086	0.44492017	0.291546211	0.500757509	0.552814652
protein56	0.550983571	0.496775038	0.089711212	0.609431834	0.950519686	0.564260335
protein57	0.588955589	0.399663477	0.268178686	0.195061129	0.677796033	0.271139318
protein58	0.528449282	0.637165612	0.388329992	0.40286496	0.498295389	0.30062392
protein59	0.601779252	0.813951251	0.972581676	0.606104355	0.99651101	0.50984962
protein60	0.358177875	0.971566658	0.939295489	0.258080793	0.046821332	0.432076408
protein61	0.215898664	0.16481797	0.267180855	0.296904479	0.536706898	0.499094133
protein62	0.721319369	0.977751638	0.399863891	0.114349684	0.191042264	0.13360937
protein63	0.526770676	0.13305538	0.528330076	0.42729097	0.899472657	0.20495134
protein64	0.74041248	0.358460646	0.013588585	0.53335124	0.196911565	0.270794911
protein65	0.423650942	0.037028606	0.029929215	0.91885699	0.944606949	0.250795396
protein66	0.013598182	0.124505757	0.098784472	0.110043485	0.336810969	0.468085919
protein67	0.875384392	0.666533999	0.998699727	0.921972974	0.269602531	0.999853779
protein68	0.389763473	0.543996193	0.453664108	0.357524658	0.256674508	0.138297241
protein69	0.989995993	0.933590185	0.728864597	0.642563731	0.63626545	0.986435677
protein70	0.344739693	0.455033467	0.277329572	0.236647829	0.99447734	0.962611081
protein71	0.344029962	0.258233081	0.27946336	0.504306631	0.059642877	0.042321403
protein72	0.990149755	0.43033956	0.727804593	0.315031256	0.428771405	0.606973588
protein73	0.980010936	0.536351496	0.792459902	0.21475268	0.497742157	0.973566377
protein74	0.029378461	0.169899454	0.490532397	0.540477243	0.17628776	0.699109742
protein75	0.024287626	0.291580497	0.153676365	0.874232996	0.735014392	0.058511081
protein76	0.23614577	0.176915025	0.614894395	0.956701471	0.822677541	0.398301527
protein77	0.872337677	0.680133671	0.276904392	0.469358016	0.020074098	0.438384384
protein78	0.702711553	0.745110836	0.481211218	0.556333357	0.861230363	0.227543124
protein79	0.496590638	0.537850551	0.24012069	0.971338596	0.666206152	0.485584098
protein80	0.805569513	0.264843593	0.728664985	0.535440314	0.459766895	0.441764153
protein81	0.72210255	0.599214674	0.693628097	0.370340448	0.012107564	0.11413817
protein82	0.058792544	0.837276592	0.535703814	0.54429201	0.351159191	0.504381629
protein83	0.945161518	0.238986507	0.699804522	0.4247302	0.754882812	0.076056326
protein84	0.058176154	0.696600805	0.112801656	0.611122357	0.630338211	0.472786578
protein85	0.4964451	0.31601527	0.255416708	0.300014553	0.284052374	0.857228019
protein86	0.661603154	0.527571481	0.898159514	0.953075851	0.370684365	0.486787466
protein87	0.675233086	0.854044781	0.633968255	0.868082896	0.006404833	0.20081543
protein88	0.176833932	0.12980006	0.059860796	0.037318478	0.923219281	0.255300512
protein89	0.336967914	0.962323181	0.585833243	0.494059335	0.659501162	0.520424374
protein90	0.114827679	0.953159749	0.641332223	0.390621256	0.977909639	0.310468422
protein91	0.36771061	0.345454185	0.447244909	0.783510116	0.510032541	0.745687023
protein92	0.990137239	0.618745078	0.221793003	0.336632617	0.207446643	0.21701026
protein93	0.672596151	0.557426961	0.23452454	0.68006612	0.328876782	0.216499769
protein94	0.43904726	0.84772286	0.728493344	0.390138814	0.959153602	0.28976034
protein95	0.744142277	0.186217811	0.029561071	0.671092008	0.097159255	0.764376307
protein96	0.841812656	0.440726883	0.90302471	0.497747151	0.13072324	0.126721984
protein97	0.20488616	0.566345413	0.316886685	0.286125691	0.042550611	0.005176815
protein98	0.990144408	0.629420237	0.162497339	0.235526658	0.133771507	0.403680368
protein99	0.54433037	0.655007858	0.473160857	0.295717332	0.347074454	0.588217328
protein100	0.558155605	0.98697914	0.950869889	0.894547726	0.914887557	0.292393484
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	gender	treatment
run1	male	drug
run2	male	no drug
run3	female	drug
run4	female	no drug
run5	male	drug
run6	female	no drug