DATCMP im Maverick

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mab
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DATCMP im Maverick

#1 Post by mab » 2014.11.14 00:04

Dear All,

I am wondering if my data format is OK or datcmp is broken. Although I tried several data formats and three recent version of datcmp. Any hint will be appreciate :

my files and output:

a.dat)

# REMARK Columns: q, I(q), error
1.185900E-02 2.14433E03 2.12911E02
1.246700E-02 2.04531E03 1.31805E02
1.307500E-02 2.01542E03 4.51282E02
1.368300E-02 2.04956E03 2.85521E02
1.429100E-02 2.06111E03 3.05166E02
1.489900E-02 2.05000E03 2.23006E02
1.550700E-02 2.06500E03 1.74990E02
1.611500E-02 2.02543E03 1.53453E02
1.672400E-02 2.02297E03 1.46936E02
... more lines follows
b.dat)
# REMARK Columns: q, I(q), error
1.185900E-02 1.95367E03 2.06718E02
1.246700E-02 1.90382E03 1.33606E02
1.307500E-02 1.84460E03 4.45725E02
1.368300E-02 1.84456E03 2.98739E02
1.429100E-02 1.82568E03 3.05721E02
1.489900E-02 1.80671E03 2.34762E02
1.550700E-02 1.79001E03 1.77641E02
1.611500E-02 1.75975E03 1.51766E02
1.672400E-02 1.74624E03 1.49467E02
....
(version 2.5.1)
Hypothesis: all data sets are similar
Alternative: at least one data set is different

Univariate Type III Repeated-Measures ANOVA
eps num Df den Df F Pr(>F) adj Pr(>F)
Assuming Sphericity 1 513 162.0400 0.000000
Greenhouse-Geyser Correction 1.0000 1 512 0.000000
Huynh-Feldt Correction 1.0000 1 512 0.000000

(version 2.5.2)
Hypothesis: all data sets are similar
Alternative: at least one data set is different

Univariate Type III Repeated-Measures ANOVA
eps num Df den Df F Pr(>F) adj Pr(>F)
Assuming Sphericity 1 513 162.5289 0.000000
Greenhouse-Geyser Correction 1.0000 1 512 0.000000
Huynh-Feldt Correction 1.0000 1 512 0.000000

(version 2.6)
% datcmp a.dat b.dat


Hypothesis: all data sets are similar
Alternative: at least one data set is different

Pair-wise Correlation Map test with correction for Familywise Error Rate (Bonferroni)
C Pr(>C) adj Pr(>C)
1 vs. 2 255.000000 0.000000 0.000000*
1 vs. 3 235.000000 0.000000 0.000000*
1 vs. 4 282.000000 0.000000 0.000000*
2 vs. 3 255.000000 0.000000 0.000000*
2 vs. 4 11.000000 0.116297 0.697785
3 vs. 4 282.000000 0.000000 0.000000*

1* 0.000000 + 1.000000 * a.dat
2 0.000000 + 1.000000 * a.dat
3 0.000000 + 1.000000 * b.dat
4 0.000000 + 1.000000 * b.dat

franke
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Re: DATCMP im Maverick

#2 Post by franke » 2014.11.14 18:40

What exactly is your question?
Release Notes wrote: Changes in Programs
====================
* datcmp: pair-wise correlation map set as default test
If you want to use the previous test, add "--test=anova", however, this is not recommended.

Code: Select all

               C      Pr(>C) adj Pr(>C)
1 vs. 2 255.000000 0.000000 0.000000*
1 vs. 3 235.000000 0.000000 0.000000*
1 vs. 4 282.000000 0.000000 0.000000*
2 vs. 3 255.000000 0.000000 0.000000*
2 vs. 4 11.000000 0.116297 0.697785
3 vs. 4 282.000000 0.000000 0.000000*
This means that only frames 2 and 4 may be considered similar, all others are different from each other. Given the large value of C, I'd say that there are scaling issues.

I'd give a link to the relevant publication here, but it's still in review :?

mab
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Re: DATCMP im Maverick

#3 Post by mab » 2014.11.14 20:46

Thanks for your comments.
Sorry I wasn't clear.

I am using datcmp v2.1 (r4556). My MAC OS is 10.9.4

I tested using a) twice the same dataset, b) fairly similar scaled datasets , b)
completely different datasets (two non-related proteins) ,

the only change in the output are filenames and Cs.

The C are large for identical (twice the same) datasets

What is going on? Is datcmp broken in my OS version?

Mario

franke
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Re: DATCMP im Maverick

#4 Post by franke » 2014.11.15 00:14

mab wrote:What is going on? Is datcmp broken in my OS version?
No, it's perfectly fine.

The point is: if two datasets are exactly identical, then the probability that this can occur by chance is, in all generality, exactly 0.0.
And this is what you see.

Going into the details here would be a bit too much, but I invite you to look up the paper once it's (finally) published. Then it should become clear. I hope.

franke
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Re: DATCMP im Maverick

#5 Post by franke » 2015.04.07 23:43

Finally, the details.

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