Chp file microarray

Accepted processed microarray files formats Important notes on file preparation: Do not compress your microarray data files. What are "processed" files? What should a processed text file look like?

Select Affymetrix. After import, Array Studio will prompt the user to attach a design table and annotation tables. The Columns section is used to specify which columns represent signal columns leave these unchecked and which columns represent descriptive columns these will be parsed as annotation table columns.

Make sure to specify the column to be used as the ID column by checking it i. The File name section is used to choose the location of the GenePix Result files for import. Sample genepix. File name section is used to choose the location of the Agilent text files for import.

Sample Agilent file. Note: Array Studio relies on the format for Agilent text files being the correct, unedited, text file format. An example format is shown below. CellMargin Size of gaps between cells in the image created from the GeneChip array, used for computing the intensity values of the cells. Rows Number of rows of probes. Cols Number of columns of probes. NumMasked Number of masked probes, which are not used in subsequent processing. NumOutliers Number of cells identified as outliers extremely high or extremely low intensity by the image-processing step.

AlgParams Character vector containing parameters used in steps required to create the CHP file for example, background correction. ChipSummary Summary information for the GeneChip array, including background average, standard deviation, max, and min. BackgroundZones Structure containing information about the zones used in the background adjustment step. ProbeSets Expression GeneChip array NumProbeSets -by-1 structure array containing information for each expression probe set, including the following fields: Name — Name of the probe set.

Name — Name of the probe set. LibSetVersion Version of a collection of related library files for a given chip. Rows Number of rows in the CEL file. Note The CLF file is 1 base, which means the first row and column are designated 1,1, not 0,0. Tip This information is useful when numbering does not start with 1. ID Identifier for the probe set gene ID.

Description Description of the probe set. SourceNames Source or sources of the probe sets. Examples collapse all Visualize Microarray Data. Open Script. CEL' ;. Image axis image. You have a modified version of this example. Do you want to open this example with your edits? No, overwrite the modified version Yes.

Select a Web Site Choose a web site to get translated content where available and see local events and offers. Information about experimental conditions and protocols captured by the Affymetrix software. Size of gaps between cells in the image created from the GeneChip array, used for computing the intensity values of the cells. Number of cells identified as outliers extremely high or extremely low intensity by the image-processing step. NumProbes -by-8 array of information about the individual probes, including intensity values.

The ProbeColumnNames field contains the column names of this array. Type of assay associated with the GeneChip array for example, Expression, Genotyping, or Resequencing.

Character vector containing parameters used in steps required to create the CHP file for example, background correction. Guidelines for the content of each field is provided on the worksheets. Incomplete submissions will result in processing delays. Recommendations for Affymetrix submissions This page contains deposit recommendations, instructions and templates specific to Affymetrix arrays.

With this submission option, you provide the following components: An Excel metadata worksheet containing descriptive information and protocols for the overall experiment and individual Samples see templates below.