Improved GUI for Affymetrix gene expression analysis

Log transform, Log ratio, Normalization, Filtering, Visualization, Noise reduction, PCA, Clustering

Description

This user interface allows a user to load some Affymetrix data in an Excel file and perform some basic operations on it - log transform, log ratio, normalization, noise reduction, filtering, PCA and clustering, in addition to some visualizations like profile plots, boxplots and matrix scatterplots.

A sample Excel data file is included, which represents 8 samples in a time series study.

Users can push buttons on the GUI in a step-by-step fashion from top to bottom

• Required Products: Bioinformatics Toolbox; Statistics Toolbox
• MATLAB release: MATLAB 7.0.4 (R14SP2)

[Sergei Vonsovskii]

Im sorry:

function editCoeff_FileLoad_Path_Callback(hObject, eventdata, handles)

fname = get(hObject,'String');
[pathstr fname ext] = fileparts(fname);
if isempty(pathstr) % Add directory if not included
pathstr = cd;
end;
if isempty(ext)
ext = '.xls';
end;
ffname = fullfile(pathstr,[fname ext]);
FileOnPath = which(ffname);
if ~isempty(fname) && exist('FileOnPath','file')
localLoadFile(handles,ffname) %Загружаем коэффициенты
else
warndlg('Неверное имя файла','Предупреждение')
return
end

[Sergei Vonsovskii]

Hello...Littel BUG ;-)

function FileEdit_Callback(hObject, eventdata, handles)
% hObject handle to FileEdit (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of FileEdit as text
% str2double(get(hObject,'String')) returns contents of FileEdit as a double
% Get file name
fname = get(hObject,'String');
[pathstr name ext] = fileparts(fname);
if isempty(pathstr) % Add directory if not included
pathstr = pwd;
end;
if isempty(ext)
ext = '.xls';
end;
fname = fullfile(pathstr,[name ext]);
localLoadFile(handles,fname) %Uses a load function to create variables

if you click 'Cancel' - no file was selected. Fix BUG:

function editCoeff_FileLoad_Path_Callback(hObject, eventdata, handles)
% hObject handle to editCoeff_FileLoad_Path (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)

% Имя файла
fname = get(hObject,'String');
[pathstr fname ext] = fileparts(fname);
if isempty(pathstr) % Add directory if not included
pathstr = cd;
end;
if isempty(ext)
ext = '.xls';
end;
ffname = fullfile(pathstr,[fname ext]);
if ~isempty(fname)
localLoadFile(handles,ffname) %Загружаем коэффициенты
else
warndlg('Неверное имя файла','Предупреждение')
return
end

AND

function pushBtn_FileLoad_Callback(hObject, eventdata, handles)
% hObject handle to pushBtn_FileLoad (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)

[fname pname] = uigetfile('*.xls');
% Обновляем editCoeff_FileLoad_Path
if fname~=0 % True unless user cancelled file load
set(handles.editCoeff_FileLoad_Path,'String',[pname fname])
localLoadFile(handles,[pname fname])
else return
end

[Amphun Chaiboonchoe]

I download Improved GUI for Affymetrix gene expression analysis

and unzip to my current Matlab folder. Afterthat I go to current directory in Matlab
and double click maGUI.fig.

Then I click step 1 download data, it o.k I can select my dataset which similar to your example but contain 54675*39 timepoints. Then afterthat nothing happen even I change dataset to your example. After click step 1 nothing happen.
So I click step 2 and then the following error return to me ;

??? Error using ==> uiimport at 69
Cannot open the Import Wizard on a file while the Import Wizard is open.

??? Error using ==> mapcaplot>localInit at 122
The number of labels should match the number of rows in the input data

Error in ==> mapcaplot at 60
    localInit(fig,varargin{:});

Error in ==> maGUI>PCA_pushbutton_Callback at 235
mapcaplot(data, genes)

Error in ==> gui_mainfcn at 95
        feval(varargin{:});

Error in ==> maGUI at 42
    gui_mainfcn(gui_State, varargin{:});

??? Error using ==> maGUI('PCA_pushbutton_Callback',gcbo,[],guidata(gcbo))
Error using ==> mapcaplot>localInit at 122
The number of labels should match the number of rows in the input data

??? Error while evaluating uicontrol Callback

Please give me some advice or suggestion.

Kindly regards,
Amphun.

P.S If I have problem with running demo of Bioinformatics tools, because I used different dataset and it different microarray platform. If  I want to follow demo but I couldn't find
the file like HuGeneFL_genesymbol_hastable this is for HuGeneFL but I use HuGeneU133P2 like this , for this kind of question whom I should contact. and when I used my own dataset follow demo so many error message occur even the command

GO = geneont('LIVE', true);
but when I run it come back with
Warning: Unknown field !synonymtypedef with value systematic_synonym "Systematic synonym" EXACT ! synonymtypedef not supported by OBO 1.0 for header information
> In geneont.geneont.geneont at 31
  In geneont.geneont at 204

Please advice who I can ask to solve and understand my problem.

[Power User]

Can not load included XLS data file. :-( It would definitely help to have some kind of help file.

[lionel bokobza]

my names is Lionel Bokobza i'm from france and i work on matlab
but i dont understand anything
please if you can help me thank you
im must input shot noise in cell ( matrice cell) and look when i can inject a seed of shot noise
and look what is the impact of the pollution and the size of the noise

if you can help me thank you very much

if not please send me an answer or send me a mail of some one who can help me

thank you

lionel

[Tao Song]