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

[Sean Davis]

An issue with GEO is that one cannot always tell for sure what has happened
to the data before submission.  Perhaps these are already log-transformed
(what base?) or centered to zero?  To know for sure, one would probably have
to contact the author, but you could plot the distribution of values for an
array and see what it looks like.

Sean


On 6/2/04 5:22, "Gong Wuming" <gongwuming at hotmail.com> wrote:

> 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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