Running this process for the
Illumina_CNV370_Samples_Confidential.txt
example generates the
Results
window shown below. Refer to the
Illumina Copy Number Input Engine
process description for more information.
Note
: For this example,
R
,
X
,
Y
,
Log_R_Ratio
,
LOH_Score
, and
CNV_Value
were specified in the
Columns to Include
option.
The
Results
window contains the following elements:
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•
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Intensity Data Set:
(Also know as the
Copy Number Data Set
or the
Output Data Set
). This data set contains the data from the input
file.
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Experimental Design Data Set (EDDS)
: This data set lists specific information about experimental details for each of the arrays. Refer to
Experimental Design Data Set (EDDS)
for more information about this data set.
Note
: There can be more that one EDDS depending on the columns specified in the
Columns to Include
option. In this example a separate EDDS was generated for analysis of data in the
Log_R_Ratio
column.
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•
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XY Data Set:
This data set contains the intensity data for the individuals in the sample. This data set only contains the X and Y measures (assuming that these measures are present in the text file exported from BeadStudio). This is a tall data set, with
SNPs
listed in rows, and individuals listed in the columns. There are two rows per SNP; one row lists the intensity value for
X
(the normalized intensity for the
A
allele
) while the second row lists the intensity value for
Y
(the normalized intensity for the
B
allele). An
Allele
column in this data set identifies the allele whose intensity is listed in each row
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•
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XY EDDS
: This data set lists experimental details needed for further analysis of the data contained in the
XY Data Set
.
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Note
: You can view the data in a file or data set by clicking either
or
(when the data set is very large).
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•
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Basic Copy Number Workflow
: Click
to launch the
Basic Copy Number Workflow
process with the output data set, EDDS, and
annotation data set
specified as input.
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Click
to reopen the completed process dialog used to generate this output.
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Click
to close all graphics windows and underlying data sets associated with the output.
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