Answers.Body: <p>The steps you describe are correct. For step 2 it is usually normalized to mean 0 and variance 1. However the "machine learning" part is important. </p>
  
  <p>Having several samples being technical replicates will make the integration task easier. However, you have too few samples to make any good prediction. At most I would describe it as an exploratory analysis.</p>
  
  <p>I recommend using regularized canonical correlation analysis for this kind of multi-omics analysis. The method seeks which are the features of one dataset that correlate (or covariate, depending on a parameter) with the variables of other datasets. Then you could use those features to predict the position of the other. </p>
  
  <p>There are several implementations of this methods, the original in the <a href="https://cran.r-project.org/package=RGCCA" rel="nofollow noreferrer">RGCCA</a> package, and <a href="https://bioconductor.org/packages/mixOmics" rel="nofollow noreferrer">mixOmics</a> for other procedures with cross-validations also <a href="https://bioconductor.org/packages/STATegRa" rel="nofollow noreferrer">STATegRa</a> has other related methods. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-08T20:02:07.693Z
Answers.LastActivityDate: 2018-11-08T20:02:07.693Z
Answers.UserDisplayName: llrs
Body: <p>I would like to use public omics datasets (ChIP-seq, RNA-seq, and ATAC-seq) from different studies to do an integrative analysis as follow:</p>
  
  <ol>
  <li>Normalise samples, within each type of omics, from different public datasets.</li>
  <li>Convert the normalised values into a uniform scale to make the comparison between ChIP-seq, RNA-seq and ATAC-seq possible.</li>
  <li>Feed the normalised uniformed values into machine learning to infer one feature (e.g. RNA expression) from other features (e.g. TF or histone marks ChIP-seq).</li>
  </ol>
  
  <p>How could I integrate these data-sets to predict one group of variables from another one?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-05T15:09:33.387Z
Comments.Text: This question is very general and opinion based.  Could you please make the question more specific
Comments.UserDisplayName: Bioathlete
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-05T16:43:23.773Z
Comments.Text: What is your goal? Do you have some data at hand? Would the data of the different omic come from the same sample or from different subjects? Would the data be quite homogeneous or not? How many samples do you have for each dataset ?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-06T05:46:52.833Z
Comments.Text: These are mouse samples, same background, so I am assuming homogeneity.
  I have at least 2 replicates per samples, where sample A --is a precursor to --> B --> C.  
  
  My goals are: 
  a) to describe the dynamic of different histone marks during differentiation (A -> B -> C). 
  b) to predict gene expression from these histone marks.
Comments.UserDisplayName: Firas
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-06T14:28:55.187Z
Comments.Text: Could you further elaborate that @Firas? How many samples do you have (6)? Do you have two replicates per A, B and C or more? Are they technical replicates or biological replicates? With a bit more of information I could possibly answer it
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-06T19:55:56.937Z
Comments.Text: If you are looking for transcription regulation, then the following article will give you a basic idea. https://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30002-8
Comments.UserDisplayName: arup
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-07T01:56:59.067Z
Comments.Text: @Llopis Many thanks, I have 5 histone chip-seq, atac-seq and RNA-seq in 2 technical replicates for each of A, B and C.
Comments.UserDisplayName: Firas
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-11-07T01:57:25.710Z
Comments.Text: @arupgsh great reference, I will look into it. Many thanks.
Comments.UserDisplayName: Firas
Tags: <rna-seq><chip-seq><atac-seq><machine-learning><multi-omics>
Title: Integrative analysis of omics studies using machine learning
ThreadText: # Integrative analysis of omics studies using machine learning
  
  (Asked by: username_0 on 2018-11-05)
  
  I would like to use public omics datasets (ChIP-seq, RNA-seq, and ATAC-seq) from different studies to do an integrative analysis as follow:
  
  1. Normalise samples, within each type of omics, from different public datasets.
  2. Convert the normalised values into a uniform scale to make the comparison between ChIP-seq, RNA-seq and ATAC-seq possible.
  3. Feed the normalised uniformed values into machine learning to infer one feature (e.g. RNA expression) from other features (e.g. TF or histone marks ChIP-seq).
  
  How could I integrate these data-sets to predict one group of variables from another one?
  
  **Tags:** rna-seq, chip-seq, atac-seq, machine-learning, multi-omics
  
  > **Comments:**
  > **username_1**: This question is very general and opinion based.  Could you please make the question more specific  
  > **username_2**: What is your goal? Do you have some data at hand? Would the data of the different omic come from the same sample or from different subjects? Would the data be quite homogeneous or not? How many samples do you have for each dataset ?  
  > **username_0**: These are mouse samples, same background, so I am assuming homogeneity. I have at least 2 replicates per samples, where sample A --is a precursor to --> B --> C.    My goals are:  a) to describe the dynamic of different histone marks during differentiation (A -> B -> C).  b) to predict gene expression from these histone marks.  
  > **username_2**: Could you further elaborate that @username_0? How many samples do you have (6)? Do you have two replicates per A, B and C or more? Are they technical replicates or biological replicates? With a bit more of information I could possibly answer it  
  > **username_3**: If you are looking for transcription regulation, then the following article will give you a basic idea. https://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30002-8  
  > **username_0**: @Llopis Many thanks, I have 5 histone chip-seq, atac-seq and RNA-seq in 2 technical replicates for each of A, B and C.  
  > **username_0**: @arupgsh great reference, I will look into it. Many thanks.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-11-08. Score: 2 | Accepted answer
  
  The steps you describe are correct. For step 2 it is usually normalized to mean 0 and variance 1. However the "machine learning" part is important.
  
  Having several samples being technical replicates will make the integration task easier. However, you have too few samples to make any good prediction. At most I would describe it as an exploratory analysis.
  
  I recommend using regularized canonical correlation analysis for this kind of multi-omics analysis. The method seeks which are the features of one dataset that correlate (or covariate, depending on a parameter) with the variables of other datasets. Then you could use those features to predict the position of the other.
  
  There are several implementations of this methods, the original in the [RGCCA](https://cran.r-project.org/package=RGCCA) package, and [mixOmics](https://bioconductor.org/packages/mixOmics) for other procedures with cross-validations also [STATegRa](https://bioconductor.org/packages/STATegRa) has other related methods.
  
  
  ---
  
  