[Bioperl-l] problem with not transformed negative numbers in .soft file of GEO database

[Gong Wuming]

Hi list,

I am afraid the question is not suitable to this mailing list, but I can 
not find better place to post it.

I have a problem with the .soft file in GEO database. 
Taking the GDS169.soft file for example, what does the negative entry mean? 
How to deal with these negative numbers before log transformation?

GDS169.soft:
...
ID_REF  IDENTIFIER  GSM2559 GSM2561 GSM2563 GSM2564 GSM2566 GSM2568 GSM2570 
GSM2572 GSM2574
IL2_at  M16762  -29 -48 -74 -30 -20 -51 -52 -80 -82
IL10_at M37897  34  28  14  34  56  34  21  51  15
GMCSF_at    X03019  -120    -53 -49 -31 -86 -29 -28 -63 -91
TNFRII_at   M60469  8   27  24  19  89  54  70  62  113
MIP1-B_at   M35590  410 421 445 426 53  142 21  12  169
IL4_at  M25892  28  23  38  7   -1  27  18  27  0
IL12_P40_at M86671  -73 -70 -104    -91 -17 -69 9   47  14
TNFa_at X02611  -13 -44 -42 -38 -13 -36 -22 -18 -53
TCRa_at M77167  -143    -109    -153    -116    -149    -225    -248    
-210    -238
AFFX-BioB-5_at  J04423  54  84  null    2   303 309 272 421 467
AFFX-BioB-M_at  J04423  95  86  null    69  394 267 386 567 430
...
...

Sincerely

Wuming Gong
College of Life Science, Wuhan University, China

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