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Mathematica > 数据处理 > 导入和导出 > Affymetrix (.cel, .cdf, .chp, .gin, .psi) >
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Affymetrix (.cel, .cdf, .chp, .gin, .psi)

Affymetrix microarray data formats.
Family of file formats used for the storage and exchange of microarray data and meta-information.
ASCII or binary formats.
Native formats of the MAS, GCOS, and Command Console applications.
CEL files store a raster of intensity values of individual probes.
CHP files contain processed information about probe sets.
CDF files describe which probes are part of which probe set.
GIN files store the gene names associated with each probe set.
PSI files store probe set names and the number of probe pairs in a probe set.
  • Import fully supports the Affymetrix CEL, CDF, CHP, GIN, and PSI formats.
IMPORT
  • Import imports data from any Affymetrix CEL, CDF, CHP, GIN, or PSI file.
  • Import imports the specified element.
  • Import imports multiple elements.
  • The import format can be specified with Import["file", "Affymetrix"] or Import.
  • See the reference pages for full general information on Import.
参数
"Elements"list of elements and options available in this file
"Rules"full list of rules for each element and option
"Options"list of rules for options, properties, and settings
  • Common data representation element:
"Data"intensity values (CEL), processed probe set data (CHP), or probe set records (CDF, PSI, GIN)
"ProbeSetNames"probe set names as a list of strings
  • When importing from CDF, PSI, or GIN, Import returns the record corresponding to the specified probe set.
  • Import uses the element by default for all Affymetrix file formats.
  • Common meta-information element:
"Header"meta-information given as list of rules
  • Additional CEL elements, representing meta-information about the underlying DAT image file:
"PixelRange"number of pixels corresponding to each probe intensity value
"DataErrors"errors in intensity values
"Outliers"list of coordinates of probes that are considered outliers
  • Additional CDF element:
"QCData"quality control information
  • Additional CHP elements:
"DetectionStates"detected gene expression state, given as a list of values True, False, Indeterminate
"DetectionSignificances"-values corresponding to each detection state
"ProbePairs"number of probe pairs in each probe set
"ProbePairsUsed"number of probe pairs used to infer detection states
"Alleles"detected genotypes
"ConfidenceValues"confidence value of each genotype detection
范例关闭所有单元
例   (5)
Import and plot a raster of intensity values from a CEL file:
Import complete header information from a CEL file:
Read complete header information from a CDF file:
Import the first few probe set names:
Import data associated with a probe set name:
Import probe set names, signal data, and the detection states from a CHP file:
Read complete header information from a GIN file:
Import the first few probe set names:
Import data associated with a probe set name:
Import the first few probe set names from a PSI file:
Import data associated with a probe set name:
Show the positions of outlier probes:
Extract the manufacturer's watermark from the data and show it as an image:
Import and plot a raster of intensity values from a CEL file:
In[1]:=
Click for copyable input
In[2]:=
Click for copyable input
Import complete header information from a CEL file:
In[3]:=
Click for copyable input
Out[3]=
 
Read complete header information from a CDF file:
In[1]:=
Click for copyable input
Out[1]=
Import the first few probe set names:
In[2]:=
Click for copyable input
Out[2]=
Import data associated with a probe set name:
In[3]:=
Click for copyable input
Out[3]=
 
Import probe set names, signal data, and the detection states from a CHP file:
In[1]:=
Click for copyable input
Out[1]=
 
Read complete header information from a GIN file:
In[1]:=
Click for copyable input
Out[1]=
Import the first few probe set names:
In[2]:=
Click for copyable input
Out[2]=
Import data associated with a probe set name:
In[3]:=
Click for copyable input
Out[3]=
 
Import the first few probe set names from a PSI file:
In[1]:=
Click for copyable input
Out[1]=
Import data associated with a probe set name:
In[2]:=
Click for copyable input
Out[2]=
Show the positions of outlier probes:
In[1]:=
Click for copyable input
Out[1]=
 
Extract the manufacturer's watermark from the data and show it as an image:
In[1]:=
Click for copyable input
Out[1]=
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