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Two
other files, besides expression are also required
by AltAnalyze to instruct the program which samples
correspond to which groups (groups file) and
which groups you want to compare (comparison file).
While these files can be produced within AltAnalyze
through the user interface by the user, for very
large datasets with hundreds of samples and dozens
of groups, the user may wish to do this outside
of AltAnalyze in Excel. When made by AltAnalyze,
the program will save two files with the prefix
"groups." and "comps" to the
same folder with the expression file (must have
the same suffix as the expression file). These
files are saved to the same directory as the expression
file. To make the groups file outside of AltAnalyze:
- Open the expression file in a
spreadsheet application such as Microsoft
Excel, OpenOffice
or Google Docs. The program should warn you
that the file is not loaded completely. This
is OK, just make
sure not to save this file.
- Once opened, copy the row containing
names of the CEL files. Note: this column
may not be the first column in the file, depending
on the program used to summarize the expression
values. Scroll down until you see a row with
column headers above the expression values.
The first column should say "probeset_id".
- Paste transpose
the column headers into a new spreadsheet.
In Microsoft Excel, this is through the menu
option Edit>Paste Special>Transpose.
Make sure only the .CEL files names appear
(not the probe set column header).
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GSM86112-0hr1.CEL
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1
|
0hr
|
|
GSM86114-0hr2.CEL
|
1
|
0hr
|
|
GSM86116-0hr3.CEL
|
1
|
0hr
|
|
GSM86118-6hr1.CEL
|
2
|
6hr
|
|
GSM86120-6hr2.CEL
|
2
|
6hr
|
|
GSM86122-6hr3.CEL
|
2
|
6hr
|
|
GSM86124-12hr1.CEL
|
3
|
12hr
|
|
GSM86126-12hr2.CEL
|
3
|
12hr
|
|
GSM86128-12hr3.CEL
|
3
|
12hr
|
|
GSM86136-4days1.CEL
|
4
|
4days
|
|
GSM86138-4days2.CEL
|
4
|
4days
|
|
GSM86140-4days3.CEL
|
4
|
4days
|
|
GSM86142-7days1.CEL
|
5
|
7days
|
|
GSM86144-7days2.CEL
|
5
|
7days
|
|
GSM86146-7days3.CEL
|
5
|
7days
|
|
GSM86154-14days1.CEL
|
6
|
14days
|
|
GSM86156-14days2.CEL
|
6
|
14days
|
|
GSM86158-14days3.CEL
|
6
|
14days
|
|
GSM86300-24hr1.CEL
|
7
|
24hr
|
|
GSM86302-24hr2.CEL
|
7
|
24hr
|
|
GSM86304-24hr3.CEL
|
7
|
24hr
|
- If the name of the expression file was "exp.mESC_differentiation.txt"
or "mESC_differentiation.txt", this
file should be saved as "groups.mESC_differentiation.txt"
or "groups." plus the name of the
experiment, to the same folder as the expression
file.
- The comparison file is simply two columns, each with a
single number. One row illustrates comparison
between the groups designated in the groups
file. In this case, we wish to compare
different time-points of differentiation to
0hr, where 0hr is the control group.
- This file should be saved as "comps.mESC_differentiation.txt",
to the same folder.
If
you have any other questions you can email us
at: alt_predictions@googlegroups.com
or
nsalomonis@gmail.com
|
