Read microarray data from ImaGene Results file
imagenedata
= imageneread(File
)
imagenedata
= imageneread(...,
'CleanColNames', CleanColNamesValue
, ...)
File | ImaGene® Results formatted file. Enter a character vector or string specifying a file name, or a path and file name. |
CleanColNamesValue | Controls the conversion of any ColumnNames containing
spaces or characters that cannot be used as MATLAB® variable names,
to valid MATLAB variable names. Choices are true or false (default). |
reads ImaGene results
data from imagenedata
= imageneread(File
)File
and creates imagenedata
,
a MATLAB structure containing the following fields.
Field |
---|
HeaderAA |
Data |
Blocks |
Rows |
Columns |
Fields |
IDs |
ColumnNames |
Indices |
Shape |
calls imagenedata
= imageneread(...,
'PropertyName
', PropertyValue
,
...)imageneread
with optional
properties that use property name/property value pairs. You can specify
one or more properties in any order. Each PropertyName
must
be enclosed in single quotation marks and is case insensitive. These
property name/property value pairs are as follows:
controls
the conversion of any imagenedata
= imageneread(...,
'CleanColNames', CleanColNamesValue
, ...)ColumnNames
containing spaces
or characters that cannot be used as MATLAB variable names, to
valid MATLAB variable names. Choices are true
or false
(default).
The field Indices
of the structure contains
indices that you can use for plotting heat maps of the data with the
function image
or imagesc
.
For more details on the ImaGene format and example data, see the ImaGene documentation.
In the following example, the file cy3.txt
is
not provided.
Read in a sample ImaGene Results file. Note that
the example file, cy3.txt
, is not provided with
the Bioinformatics Toolbox™ software.
cy3Data = imageneread('cy3.txt');
Plot the signal mean.
maimage(cy3Data,'Signal Mean');
Read in a sample ImaGene Results file. Note that
the example file, cy5.txt
, is not provided with
the Bioinformatics Toolbox software.
cy5Data = imageneread('cy5.txt');
Create a loglog plot of the signal median from two ImaGene Results files.
sigMedianCol = find(strcmp('Signal Median',cy3Data.ColumnNames)); cy3Median = cy3Data.Data(:,sigMedianCol); cy5Median = cy5Data.Data(:,sigMedianCol); maloglog(cy3Median,cy5Median,'title','Signal Median');
gprread
| ilmnbsread
| maboxplot
| maimage
| sptread