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h1. |
Why
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Do
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I
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Get
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an
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Error
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Message
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When
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Attempting
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to
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Validate
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an
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Illumina
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SNP
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Data
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File
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in
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caArray?
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Problem:
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When
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attempting
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to
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validate
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an
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Illumina
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Genotyping
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Processed
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Matrix
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SNP
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data
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TXT
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file
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based
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on
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the
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HumanHap550v3_A
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design
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in
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caArray,
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you
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may
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receive
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the
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following
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error
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message:
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"1
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data
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file(s)
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are
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in
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a
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format
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not
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currently
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supported
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for
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parsing.
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These
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files
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may
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only
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be
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included
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for
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validation
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when
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validating
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an
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SDRF
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that
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refers
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to
...
the
...
files."
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Topic
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:
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caArray
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Usage
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Release
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:
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caArray
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2.0
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and
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above
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Date
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entered
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:
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09/01/2011
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Solution
The Illumina SNP data file must be edited before it can be validated by caArray. Specifically, the data table header descriptions in the first row must be altered as follows:
- Original (invalid): "ID_REF VALUE GC_SCORE Theta R B_Allele_Freq
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- Log_R_Ratio"
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- Revised
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- (valid)
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- :
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- "ID_REF
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- GSM302898
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- GC_SCORE
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- Theta
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- R
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- B_Allele_Freq
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- Log_R_Ratio"
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The
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revision
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can
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be
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done
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in
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any
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plain
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text
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editor
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such
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as
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Windows
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Notepad.
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If,
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after
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revising
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the
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TXT
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file
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and
...
attempting
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to
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validate
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it
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again,
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you
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still
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receive
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the
...
same
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error
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message,
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check
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the
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version
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of
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your
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caArray
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installation.
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If
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you
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are
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running
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v2.3,
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upgrade
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to
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v2.4,
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then
...
repeat
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the
...
validation
...
procedure.
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Have
...
a
...
comment?
...
Please
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leave
...
your
...
comment
...
in
...
the
...
...
...
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Forum|https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=6&sid=d297ed62850db647e795b9aa1d18cb7f].
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