MATLAB Central Newsreader - help with DataMatrix objects

help with DataMatrix objects

Ugo — Fri, 20 Feb 2009 12:14:01 -0500

Dear all,
I created a DataMatrix Object with my microarray data. I am trying to find a subset (~2000) of all the probesetIDs on the DataMatrix Object. I have the probesetIDs I am interested in a cell variable. It is easy for me (consider I am a biologist!) to work with 2 cells but how can I extract specific probsetIDs, and their values, from a DataMatrix Object?
Thank you for your help

Ugo

Re: help with DataMatrix objects

Lucio Andrade-Cetto — Fri, 20 Feb 2009 14:11:03 -0500

Ugo:
Here is an example on how to extract specific probsetIDs:

Variable d is a DataMatrix
>> d =

                Sample1 Sample2 Sample3 Sample4
    Feature1 71 72 73 74
    Feature2 81 82 83 84
    Feature3 91 92 93 94
    Feature4 101 142 143 144
Feature5 151 152 153 154

To subset with row names and column names:
>> d({'Feature1', 'Feature4'},{'Sample1', 'Sample3'})

ans =

                Sample1 Sample3
    Feature1 71 73
    Feature4 101 143

To extract only the values of a subset with row names and column names:
>> d.({'Feature1', 'Feature4'})({'Sample1', 'Sample3'})

ans =

    71 73
   101 143

Or
>>rowIdx ={'Feature1', 'Feature4'};
>> colIdx ={'Sample2', 'Sample4'};

>> d(rowIdx,colIdx)

ans =

                Sample2 Sample4
    Feature1 72 74
    Feature4 142 144

>> d.(rowIdx)(colIdx)

ans =

    72 74
   142 144

The indexing can be a numeric or logical vector like other MATLAB arrays, or cell arrays of strings for indexing.

One more thing, the colon operator should work also:

>> d(rowIdx, :)

ans =

                Sample1 Sample2 Sample3 Sample4
    Feature1 71 72 73 74
    Feature4 101 142 143 144

>> d.(rowIdx)(':') %Colon is in single quote – ‘:’

ans =

    71 72 73 74
   101 142 143 144

Let me know if this solves your question.
Lucio

"Ugo " <borello.ugo@ijm.jussieu.fr> wrote in message <gnm6q9$s6v$1@fred.mathworks.com>...
> Dear all,
> I created a DataMatrix Object with my microarray data. I am trying to find a subset (~2000) of all the probesetIDs on the DataMatrix Object. I have the probesetIDs I am interested in a cell variable. It is easy for me (consider I am a biologist!) to work with 2 cells but how can I extract specific probsetIDs, and their values, from a DataMatrix Object?
> Thank you for your help
>
> Ugo

Re: help with DataMatrix objects

Lucio Andrade-Cetto — Fri, 20 Feb 2009 14:16:03 -0500

You can also find more information here on how to use the DataMatrix object here:
http://www.mathworks.com/access/helpdesk/help/toolbox/bioinfo/ug/brsyo6j.html
Lucio

"Ugo " <borello.ugo@ijm.jussieu.fr> wrote in message <gnm6q9$s6v$1@fred.mathworks.com>...
> Dear all,
> I created a DataMatrix Object with my microarray data. I am trying to find a subset (~2000) of all the probesetIDs on the DataMatrix Object. I have the probesetIDs I am interested in a cell variable. It is easy for me (consider I am a biologist!) to work with 2 cells but how can I extract specific probsetIDs, and their values, from a DataMatrix Object?
> Thank you for your help
>
> Ugo

Re: help with DataMatrix objects

Ugo — Fri, 20 Feb 2009 14:45:04 -0500

Thank you Lucio.
So if:
a=cell variable containing my probesetIDs list
d=your datamatrix object variable
What will be a simple 'for' loop to find the indices in d of the corresponding probesetIDs of A?
Thank you for your help.

Ugo