Saml Response is Assertion xml with digital signature,
so , when get xml of Saml XML, and your x509 certificate,
you can use follow code to sign it.

Here is examples.
http://msdn.microsoft.com/en-us/library/ms229745%28v=vs.110%29.aspx

using System;
using System.Security.Cryptography;
using System.Security.Cryptography.Xml;
using System.Xml;

public class SignXML
{

    public static void Main(String[] args)
    {
        try
        {
            // Create a new CspParameters object to specify 
            // a key container.
            CspParameters cspParams = new CspParameters();
            cspParams.KeyContainerName = "XML_DSIG_RSA_KEY";

            // Create a new RSA signing key and save it in the container. 
            RSACryptoServiceProvider rsaKey = new RSACryptoServiceProvider(cspParams);

            // Create a new XML document.
            XmlDocument xmlDoc = new XmlDocument();

            // Load an XML file into the XmlDocument object.
            xmlDoc.PreserveWhitespace = true;
            xmlDoc.Load("test.xml");

            // Sign the XML document. 
            SignXml(xmlDoc, rsaKey);

            Console.WriteLine("XML file signed.");

            // Save the document.
            xmlDoc.Save("test.xml");



        }
        catch (Exception e)
        {
            Console.WriteLine(e.Message);
        }
    }


    // Sign an XML file.  
    // This document cannot be verified unless the verifying  
    // code has the key with which it was signed. 
    public static void SignXml(XmlDocument xmlDoc, RSA Key)
    {
        // Check arguments. 
        if (xmlDoc == null)
            throw new ArgumentException("xmlDoc");
        if (Key == null)
            throw new ArgumentException("Key");

        // Create a SignedXml object.
        SignedXml signedXml = new SignedXml(xmlDoc);

        // Add the key to the SignedXml document.
        signedXml.SigningKey = rsaKey;

        // Create a reference to be signed.
        Reference reference = new Reference();
        reference.Uri = "";

        // Add an enveloped transformation to the reference.
        XmlDsigEnvelopedSignatureTransform env = new XmlDsigEnvelopedSignatureTransform();
        reference.AddTransform(env);

        // Add the reference to the SignedXml object.
        signedXml.AddReference(reference);

        // Compute the signature.
        signedXml.ComputeSignature();

        // Get the XML representation of the signature and save 
        // it to an XmlElement object.
        XmlElement xmlDigitalSignature = signedXml.GetXml();

        // Append the element to the XML document.
        xmlDoc.DocumentElement.AppendChild(xmlDoc.ImportNode(xmlDigitalSignature, true));

    }
}


http://www.codeproject.com/Articles/56640/Performing-a-SAML-Post-with-C
public static XmlElement SignDoc(XmlDocument doc, X509Certificate2 cert2, 
              string referenceId, string referenceValue) {
    SamlSignedXml sig = new SamlSignedXml(doc, referenceId);
    // Add the key to the SignedXml xmlDocument. 
    sig.SigningKey = cert2.PrivateKey;

    // Create a reference to be signed. 
    Reference reference = new Reference();

    reference.Uri = String.Empty;
    reference.Uri = "#" + referenceValue;

    // Add an enveloped transformation to the reference. 
    XmlDsigEnvelopedSignatureTransform env = new
        XmlDsigEnvelopedSignatureTransform();
    XmlDsigC14NTransform env2 = new XmlDsigC14NTransform();

    reference.AddTransform(env);
    reference.AddTransform(env2);

    // Add the reference to the SignedXml object. 
    sig.AddReference(reference);

    // Add an RSAKeyValue KeyInfo
    // (optional; helps recipient find key to validate). 
    KeyInfo keyInfo = new KeyInfo();
    KeyInfoX509Data keyData = new KeyInfoX509Data(cert2);

    keyInfo.AddClause(keyData);
    
    sig.KeyInfo = keyInfo;

    // Compute the signature. 
    sig.ComputeSignature();

    // Get the XML representation of the signature
    // and save it to an XmlElement object. 
    XmlElement xmlDigitalSignature = sig.GetXml();

    return xmlDigitalSignature;
}

Signed xml sample:
http://www.aleksey.com/xmlsec/api/xmlsec-examples-sign-x509.html