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Expression matrix

Expression matrices are numerical structures used to store expression data for many genomic features (genes, transcripts, exons...) form several samples (usually microarrays).

Babelomics arranges features in rows and samples in columns.

The firs column of the matrix contains a name or ID for the genomic feature in each row. The first row of the file contains a name or ID for the sample.

These values are usually stored in tab delimited text files; meaning that the columns of the file are separated by the TAB character.

In the upper left top corner of the matrix the tag #NAMES is used by Babelomics to indicate that IDs are present in the matrix.

In the firs rows of the file there may be some comment lines starting by #.

An example expression matrix file will look something like this:

#NUMBER_FEATURES    12625
#NUMBER_SAMPLES    3
#NAMES    GSM34379.CEL    GSM34385.CEL    GSM34383.CEL
AFFX-PheX-3_at    10.27238    10.27238    10.27238
AFFX-ThrX-5_at    8.04141    8.18539    8.18539
AFFX-ThrX-M_at    7.05535    6.99982    7.18862
31307_at    5.99929    5.99929    5.99929
31308_at    7.40242    7.40242    7.40242
31309_r_at    6.38979    5.88443    5.88443
31310_at    7.54131    7.51986    7.51986
31314_at    7.55259    7.55259    7.55651
31315_at    10.05357    10.05357    10.05357
31316_at    6.03735    5.9471    6.03735
31317_r_at    10.6844    10.81617    11.11591
31318_at    6.15813    6.15813    6.13989
31319_at    9.35508    9.35508    9.2556
31320_at    11.87319    11.87319    11.9407
31321_at    8.08177    8.08177    8.08177
31322_at    7.16563    7.16563    7.16563
31323_r_at    11.62011    10.83077    10.81338
31324_at    8.18443    8.24817    8.43197
31329_at    6.65331    6.33573    6.34145
...
...

Yo can also add some VARIABLES to work with, VARIABLES can be CATEGORICAL, NUMERIC AND STRING:

# some comments
# more comments
#VARIABLE tumor CATEGORICAL{ALL,AML} VALUES{ALL,ALL,ALL,AML,AML,AML}
#VARIABLE resp_treatment CATEGORICAL{Y,N} VALUES{Y,N,N,N,Y,Y}
#NAMES Cond1 Cond2 Cond3 Cond4 Cond5 Cond6
gen1    -3.06    -2.25    -1.15    -6.64    0.40    1.08
gen2    -1.36    -0.67    -0.17    -0.97    -2.32    -5.06
gen3    -0.17    0.48    1.23    1.52    1.11    
gen4        1.61    -0.27    0.71    -0.62    0.14
gen5    2.09    2.12    2.62    1.95    1.04    2.18
gen6    0.20    -3.06    -0.03    0.64    0.84    
gen7    -2.00    -0.64    -0.29    0.08    -1.00    
gen8    0.93    1.29    -0.23    -0.74    -2.00    -1.25
gen9    0.88    0.31    -0.22    3.25        
gen10    0.71    1.03    -0.25        1.03    
...
...