I would simply have more identifying columns.

• ArrayId
• ArrayIndexX
• ArrayIndexY (If necessary for 2 dimensional arrays)
• Value

this will allow you to have one table that will not need to have additional columns added to it, despite the size of data you need to store.

Storing thousands/or millions of recoreds really isn't that big of a deal assuming the columns are properly indexed.

good luck

Pack the array of double into a different property on the model and save the serialized data. The fastest packing algorithm is http://nuget.org/packages/protobuf-net. I use the following in a production app that stores around 4.5million+ in the array.

Note, I stripped this down to the bare minimum, you would probably want to optimize the Pack/Unpack calls so they dont happen on every property access.

In the example below, we save Surface to the database, which contains an array of Scans, which contains an array of samples. The same concept applies to properties of double[].

[ProtoBuf.ProtoContract]
public class Sample
{
    public Sample()
    {
    }

    [ProtoBuf.ProtoMember(2)]
    public double Max { get; set; }

    [ProtoBuf.ProtoMember(3)]
    public double Mean { get; set; }

    [ProtoBuf.ProtoMember(1)]
    public double Min { get; set; }
}

[ProtoBuf.ProtoContract]
public class Scan
{
    public Scan()
    {
    }

    [ProtoBuf.ProtoMember(1)]
    public Sample[] Samples { get; set; }
}

public class Surface
{
    public Surface()
    {
    }

    public int Id { get; set; }

    public byte[] ScanData { get; set; }

    [NotMapped]
    public Scan[] Scans
    {
        get
        {
            return this.Unpack();
        }
        set
        {
            this.ScanData = this.Pack(value);
        }
    }

    private byte[] Pack(Scan[] value)
    {
        using (var stream = new MemoryStream())
        {
            ProtoBuf.Serializer.Serialize(stream, value);
            return stream.ToArray();
        }
    }

    private Scan[] Unpack()
    {
        using (var stream = new MemoryStream(this.ScanData))
        {
            return ProtoBuf.Serializer.Deserialize<Scan[]>(stream);
        }
    }
}

You should use a separate table

You should't be trying to do hacky formatting things with your data, it will make it a lot harder to tell what you are trying to do and make what you are trying to do at a functional level get confused

Why you need a another table

The reason you need a linking table is because you have no idea how much data you are going to be holding, even if you put it into a blob there if a chance you might exceed the maximum amount of data that can be held in the blob.

The Code

I want to make a separate object for the Absorption point and store it in a Dictionary, this way if you have some sort of default case that occurs frequently (like when nothing is found at a point) you don't need to store the entire thing.

With though it would be best if you made a separate class to represent the collection, that way if someone reuses the class and doesn't know what is going on they won't be adding unnecessary data.

public class SpectroscopyObject
{
     private FrequencyAbsorptionPointCollection _freqs = new FrequencyAbsorptionPointCollection ();
     public FrequencyAbsorptionPointCollection FrequecyAbsorption {get{ return _freqs;}}
     public int Id {get;set;}

     //other stuff...
} 

public struct Point 
{
    public int X {get;set;}
    public int Y {get;set;}

    public Point ( int x , int y ) 
    {
            X = x;
            Y = y;
    }
}

public class FrequencyAbsorptionPoint
{
    public double Frequency { get; set; }
    public Point Location { get; set; }
}

public class FrequencyAbsorptionPointCollection : IEnumerable<FrequencyAbsorptionPoint>
{
    private readonly Dictionary<int , Dictionary<int , FrequencyAbsorptionPoint>> _points = new Dictionary<int , Dictionary<int , FrequencyAbsorptionPoint>> ( ); 

    int _xLeftMargin , _xRightMargin , _yTopMargin , _yBottomMargin;
    public FrequencyAbsorptionPointCollection (int xLeftBound,int xRightBound,int yTopBound,int yBottomBound)
    {
        _xLeftMargin = xLeftBound;
        _xRightMargin = xRightBound;
        _yTopMargin = yTopBound;
        _yBottomMargin = yBottomBound;
    }

    private bool XisSane(int testX)
    {
        return testX>_xLeftMargin&&testX<_xRightMargin;
    }


    private bool YisSane(int testY)
    {
        return testY>_yBottomMargin&&testY<_yTopMargin;
    }

    private bool PointIsSane(Point pointToTest)
    {
        return XisSane(pointToTest.X)&&YisSane(pointToTest.Y);
    }

    private const double DEFAULT_ABSORB_VALUE= 0.0;
    private bool IsDefaultAbsorptionFrequency(double frequency)
    {
        return frequency.Equals(DEFAULT_ABSORB_VALUE);
    }

    //I am assuming default to be 0

    public FrequencyAbsorptionPointCollection 
        (int xLeftBound,
         int xRightBound,
         int yTopBound,
         int yBottomBound,
         IEnumerable<FrequencyAbsorptionPoint> collection )
        :this(xLeftBound,xRightBound,yTopBound,yBottomBound)
    {
        AddCollection ( collection );
    }

    public void AddCollection ( IEnumerable<FrequencyAbsorptionPoint> collection ) 
    {
        foreach ( var point in collection )
        {
            Dictionary<int , FrequencyAbsorptionPoint> _current = null;
            if ( !_points.ContainsKey ( point.Location.X ) )
            {
                _current = new Dictionary<int , FrequencyAbsorptionPoint> ( );
                _points.Add ( point.Location.X , _current );
            }
            else
                _current = _points [ point.Location.X ];

            if ( _current.ContainsKey ( point.Location.Y ) )
                _current [ point.Location.Y ] = point;
             else
                _current.Add ( point.Location.Y , point );
        }
    }

    public FrequencyAbsorptionPoint this [ int x , int y ] 
    {
         get 
         {
            if ( XisSane ( x ) && YisSane ( y ) )
            {
                if ( _points.ContainsKey ( x ) && _points [ x ].ContainsKey ( y ) )
                    return _points [ x ] [ y ];
                else
                    return new FrequencyAbsorptionPoint
                {
                    Id = 0 ,
                    Location = new Point ( x , y ) ,
                    Frequency = DEFAULT_ABSORB_VALUE
                };
            }
            throw new IndexOutOfRangeException (
                string.Format( "Selection ({0},{1}) is out of range" , x , y ));
        }
        set 
        {
            if ( XisSane ( x ) && YisSane ( y ) ) 
            {
                if ( !IsDefaultAbsorptionFrequency ( value.Frequency ) ) 
                {
                    Dictionary<int,FrequencyAbsorptionPoint> current = null;
                    if ( _points.ContainsKey ( x ) )
                        current = _points [ x ];
                    else
                    {
                        current = new Dictionary<int,FrequencyAbsorptionPoint>();
                        _points.Add ( x , current );
                    }

                    if ( current.ContainsKey ( y ) )
                        current [ y ] = value;
                    else
                    {
                        current.Add ( y , value );
                    }
                }
            }
        }
    }

    public FrequencyAbsorptionPoint this [ Point p ] 
    {
        get 
        {
            return this [ p.X , p.Y ];
        }
        set 
        {
            this [ p.X , p.Y ] = value;
        }
    }

    public IEnumerator<FrequencyAbsorptionPoint> GetEnumerator ( )
    {
        foreach ( var i in _points.Keys )
            foreach ( var j in _points [ i ].Keys )
                yield return _points [ i ] [ j ];
    }

    System.Collections.IEnumerator System.Collections.IEnumerable.GetEnumerator ( )
    {
        return GetEnumerator ( );
    }
}

Now, the sql code

CREATE TABLE SpectroscopyObject
(
    Id INT PRIMARY KEY NOT NULL,
    --other stuff
) 

CREATE TABLE FrequencyAbsorptionInfo 
(
    Id INT PRIMARY KEY NOT NULL IDENTITY,
    XCoord INT NOT NULL,
    YCoord INT NOT NULL,
    AbsorptionInfo NUMERIC(5,5) NOT NULL,
    SpectroscopyObjectId INT NOT NULL 
        FOREIGN KEY REFERENCES SpectroscopyObject(Id)
)

Now all you need to do is store the points and reference your the related object with the id of the object, if you wanted to read it it would look like this

string commandStringSObjs = 
@"
SELECT Id, ..other attributes... FROM SpectroscopyObject
";
string commandStringCoords = 
@"
SELECT XCoord,YCoord,AbsorptionInfo 
WHERE SpectroscopyObjectId = @Id
";

var streoscopicObjs = new List<SpectroscopyObject>();
using(var connection = new SqlConnection(CONNECTION_STRING))
{
    using(var cmd = connection.CreateCommand())
    {
        cmd.CommandText = commandStringSObjs;
        connection.Open();
        using(var rdr = cmd.ExecuteReader())
        {
            while(rdr.Read())
            {

                streoscopicObjs.Add(new SpectroscopyObject
                {
                    Id = Convert.ToInt32(rdr["Id"])
                    //populate your other stuff
                }
            }
        }
    }
    //to read the absorption info
    foreach(var obj in streoscopicObjs)
    {
        var current = obj.FrequecyAbsorption;
        using(var cmd = connection.CreateCommand())
        { 
            cmd.CommandText = commandStringCoords;
            cmd.Parameters.Add(
                new SqlParameter("Id",DbType.Int){ Value = obj.Id});
            using(var rdr = cmd.ExecuteReader())
            {
                while(rdr.Read())
                {
                    var x = Convert.ToInt32(rdr["XCoord"]);
                    var y = Convert.ToInt32(rdr["YCoord"]);
                    var freq = Convert.ToDouble(rdr["AbsorptionInfo"]);

                    current[x][y] = new FrequencyAbsorptionPoint
                    {
                        Location = new Point(x,y),
                        Frequency = freq
                    };
                }
            }
        }
    }

    //do some stuff
    ...
   // assuming you update 
    string updatefreq = 
@"


INSERT INTO FrequencyAbsorptionInfo(XCoord,YCoord,
                   AbsorptionInfo,SpectroscopyObjectId )
VALUES(@xvalue,@yvalue,@freq,@Id) ";
    //other point already

    //to write the absorption info
    foreach(var obj in streoscopicObjs)
    {
        using(var cmd = connection.CreateCommand())
        {
            cmd.CommandText = 
@"
DELETE FrequencyAbsoptionInfo 
WHERE  SpectroscopyObjectId =@Id
";
            cmd.Parameters.Add(new SqlParameter("Id",DbType.Int){ Value = obj.Id});
            cmd.ExecuteNonQuery();
        }
        var current = obj.FrequecyAbsorption;
        foreach(var freq in current)
        {
            using(var cmd = connection.CreateCommand())
            { 
                cmd.CommandText = updatefreq ;
                cmd.Parameters.AddRange(new[]
                {
                    new SqlParameter("Id",DbType.Int){ Value = obj.Id},
                    new SqlParameter("XCoords",DbType.Int){ Value = freq.Location.X},
                    new SqlParameter("YCoords",DbType.Int){ Value = freq.Location.Y},
                    new SqlParameter("freq",DbType.Int){ Value = freq.Frequency },
                });
                cmd.ExecuteNonQuery();
            }
        }
    }
}