GeenaR: R based Spectra Analysis: Hot to run the example

Welcome to GeenaR, a tool for MALDI/ToF MS spectra analysis.

Using GeenaR for analysing MALDI spectra should be straightforward.
This page may help you in running GeenaR with the example files provided for testing purposes.
See also the help page and the page with information on file formats.

Introduction

In order to support the execution of a test run, we provide an example dataset and a related example target file.
The dataset is pre-loaded on the server in an appropriate folder and you don't need to download and/or upload it again.
On the contrary, the target file must be downloaded to your machine and uploade when you want to run the test.
Here below you may find a description of the files and a step-by-step guide for launching the test.
Note! This step-by-step guide only applies to the example dataset! See the help page for information on how to run GeenaR with your own data.

Files

A dataset including spectra from a study on colorectal cancer
The dataset includes 40 spectra from 10 samples (each sample is represented by four technical replicates). Six samples refer to sera from patients affected by colorectal cancer (various grade and stage), and the remaining four samples refer to sera from healthy volunteers.
You may download the dataset from here.

Here is a summary of the spectra with information on the originating sample.

Spectrum	File name	Sample	Replica number	Status
13S13569_A_SP	13S13569_A_SP.txt	13S13569	1	Healthy volunteer
13S13569_B_SP	13S13569_B_SP.txt	13S13569	2	Healthy volunteer
13S13569_C_SP	13S13569_C_SP.txt	13S13569	3	Healthy volunteer
13S13569_D_SP	13S13569_D_SP.txt	13S13569	4	Healthy volunteer
13S14986_A_SP	13S14986_A_SP.txt	13S14986	1	Healthy volunteer
13S14986_B_SP	13S14986_B_SP.txt	13S14986	2	Healthy volunteer
13S14986_C_SP	13S14986_C_SP.txt	13S14986	3	Healthy volunteer
13S14986_D_SP	13S14986_D_SP.txt	13S14986	4	Healthy volunteer
13S15816_A_SP	13S15816_A_SP.txt	13S15816	1	Healthy volunteer
13S15816_B_SP	13S15816_B_SP.txt	13S15816	2	Healthy volunteer
13S15816_C_SP	13S15816_C_SP.txt	13S15816	3	Healthy volunteer
13S15816_D_SP	13S15816_D_SP.txt	13S15816	4	Healthy volunteer
13S15947_A_SP	13S15947_A_SP.txt	13S15947	1	Healthy volunteer
13S15947_B_SP	13S15947_B_SP.txt	13S15947	2	Healthy volunteer
13S15947_C_SP	13S15947_C_SP.txt	13S15947	3	Healthy volunteer
13S15947_D_SP	13S15947_D_SP.txt	13S15947	4	Healthy volunteer
C103_A_SP	C103_A_SP.txt	C103	1	Colorectal affected
C103_B_SP	C103_B_SP.txt	C103	2	Colorectal affected
C103_C_SP	C103_C_SP.txt	C103	3	Colorectal affected
C103_D_SP	C103_D_SP.txt	C103	4	Colorectal affected
C128_A_SP	C128_A_SP.txt	C128	1	Colorectal affected
C128_B_SP	C128_B_SP.txt	C128	2	Colorectal affected
C128_C_SP	C128_C_SP.txt	C128	3	Colorectal affected
C128_D_SP	C128_D_SP.txt	C128	4	Colorectal affected
C131_A_SP	C131_A_SP.txt	C131	1	Colorectal affected
C131_B_SP	C131_B_SP.txt	C131	2	Colorectal affected
C131_C_SP	C131_C_SP.txt	C131	3	Colorectal affected
C131_D_SP	C131_D_SP.txt	C131	4	Colorectal affected
C132_A_SP	C132_A_SP.txt	C132	1	Colorectal affected
C132_B_SP	C132_B_SP.txt	C132	2	Colorectal affected
C132_C_SP	C132_C_SP.txt	C132	3	Colorectal affected
C132_D_SP	C132_D_SP.txt	C132	4	Colorectal affected
C133_A_SP	C133_A_SP.txt	C133	1	Colorectal affected
C133_B_SP	C133_B_SP.txt	C133	2	Colorectal affected
C133_C_SP	C133_C_SP.txt	C133	3	Colorectal affected
C133_D_SP	C133_D_SP.txt	C133	4	Colorectal affected
C135_A_SP	C135_A_SP.txt	C135	1	Colorectal affected
C135_B_SP	C135_B_SP.txt	C135	2	Colorectal affected
C135_C_SP	C135_C_SP.txt	C135	3	Colorectal affected
C135_D_SP	C135_D_SP.txt	C135	4	Colorectal affected

A target file
The target file includes a list of the spectra in the dataset with related information on sample, replica number and status, appropriately formatted.

Here is the target file:

13S13569_A_SP.txt	13S13569	1	N
13S13569_B_SP.txt	13S13569	2	N
13S13569_C_SP.txt	13S13569	3	N
13S13569_D_SP.txt	13S13569	4	N
13S14986_A_SP.txt	13S14986	1	N
13S14986_B_SP.txt	13S14986	2	N
13S14986_C_SP.txt	13S14986	3	N
13S14986_D_SP.txt	13S14986	4	N
13S15816_A_SP.txt	13S15816	1	N
13S15816_B_SP.txt	13S15816	2	N
13S15816_C_SP.txt	13S15816	3	N
13S15816_D_SP.txt	13S15816	4	N
13S15947_A_SP.txt	13S15947	1	N
13S15947_B_SP.txt	13S15947	2	N
13S15947_C_SP.txt	13S15947	3	N
13S15947_D_SP.txt	13S15947	4	N
C103_A_SP.txt	C103	1	D
C103_B_SP.txt	C103	2	D
C103_C_SP.txt	C103	3	D
C103_D_SP.txt	C103	4	D
C128_A_SP.txt	C128	1	D
C128_B_SP.txt	C128	2	D
C128_C_SP.txt	C128	3	D
C128_D_SP.txt	C128	4	D
C131_A_SP.txt	C131	1	D
C131_B_SP.txt	C131	2	D
C131_C_SP.txt	C131	3	D
C131_D_SP.txt	C131	4	D
C132_A_SP.txt	C132	1	D
C132_B_SP.txt	C132	2	D
C132_C_SP.txt	C132	3	D
C132_D_SP.txt	C132	4	D
C133_A_SP.txt	C133	1	D
C133_B_SP.txt	C133	2	D
C133_C_SP.txt	C133	3	D
C133_D_SP.txt	C133	4	D
C135_A_SP.txt	C135	1	D
C135_B_SP.txt	C135	2	D
C135_C_SP.txt	C135	3	D
C135_D_SP.txt	C135	4	D

Running the test

In order to run the test, you must execute the following steps in the the GeenaR home page.

Download the target file
The target file is available at http://proteomics.hsanmartino.it/geenar/uploads/testTargetFile.txt.
You don't need to download and/or upload the dataset, it is already pre-loaded on the server in an appropriate folder.

Fill in the 'Job information section' in the GeenaR home page

You must specify 'example' as dataset name.
You should include your email address.
You can specify any job name or leave the suggested name.
You can specify your country or leave the field empty.

Job information
^*Job name:		You can specify any job name or leave the suggested name
^*Data set name:		You must specify 'example' as dataset name
^*Email:		You should include your email address
Country:		You can specify your country or leave the field empty

Fill in the 'Input data section' in the GeenaR home page

You must select the test target file that you have downloaded for the 'Target file' field.
You can specify any allowed value for the fields 'Trimming From', 'Trimming To', Quality conitrol', 'Reporting', and 'With code' or leave them unchanged.
You should leave unspecified the 'Attribute file' (for semplicity sake).

Input data

You must select a properly formatted file from your computer. This file will be uploaded to the server but removed as soon as it is used. ^*Target file: You must select the test target file that you have downloaded.

Mass spectra can be trimmed both at the beginning and at the end of the m/z range. Here you can specify the lower and higher m/z values for the desired analysis range. Insert 0 in both fields if you do not want any trimming. Trimming: From: m/z You can specify any allowed value or leave this field unchanged.

To: m/z You can specify any allowed value or leave this field unchanged.

Mass spectra can be checked for the presence of outliers (atipicality score) and their formal correctness. When required by selecting this checkbox, quality control is carried out twice, before and after trimming. Quality control: If you select this checkbox, a report, including all results, as well as the list of methods and parameters selected, will be made available at the end of the analysis. The report is created in HTML, with and without R code. Reporting: With code: You can specify any allowed value or leave these fields unchanged.

You must select a properly formatted file from your computer. This file will be uploaded to the server but removed as soon as it is used. Attributes file: You should leave this field unspecified (for semplicity sake).

Launch the execution of GeenaR in the GeenaR home page
Just click on the button that is located below the 'Input data' section in the GeenaR home page.

That's all. Please do not hesitate to get in touch with us for any further information or clarification.

For information, get in touch with:
Paolo Romano, Bioinformatics, IRCCS Ospedale Policlinico San Martino,
Email to Paolo.Romano@HSanMartino.it
Email to gabriela.coronel@HSanMartino.it