ValueError: <type 'exceptions.ValueError'>

[Fiona Whelan]

Good morning,

I was hoping you might be able to help me out with an error that I am getting from lsa_compute:

$ lsa_compute eLSA.txt eLSA.theo.lsa -r 1 -s 26 -p theo -x 1000 -f none -n percentileZ -e eLSA.txt -m 0 -d 3
lsa_compute (rev: ) - copyright Li Charlie Xia, [e-mail]
delayLimit      minOccur        fillMethod      pvalueMethod    precision       dataFile        extraFile       resultFile      repNum  spotNum bootNum transFunc       normMethodapproxVar        trendThresh
3       0       none    theo    1000    eLSA.txt        eLSA.txt        eLSA.theo.lsa   1       26      0       simple  percentileZ     1       None
ValueError: <type 'exceptions.ValueError'>

This is in comparison to the first call in test.sh that finishes successfully:

$ lsa_compute ARISA20.csv ARISA20.theo.lsa -r 1 -s 127 -d 3 -p theo -x 1000 -f none -n percentileZ -e ARISA20.csv -m 0
lsa_compute (rev: ) - copyright Li Charlie Xia, [e-mail]
delayLimit      minOccur        fillMethod      pvalueMethod    precision       dataFile        extraFile       resultFile      repNum  spotNum bootNum transFunc       normMethodapproxVar        trendThresh
3       0       none    theo    1000    ARISA20.csv     ARISA20.csv     ARISA20.theo.lsa        1       127     0       simple  percentileZ     1       None
(19, 127)
firstData factorNum, repNum, spotNum = 19, 1, 127
secondData factorNum, repNum, spotNum = 19, 1, 127
inside applyAnalysis...
computing p_table with Rmax= 50
pairwise calculation...
LS Qvalues...
PCC Qvalues...
SCC Qvalues...
SPCC Qvalues...
SSCC Qvalues...
finishing up...
time elapsed 5.734581 seconds

The beginning of my input file:

#       MPNH82  MPNH36  MPNH37  MPNH83  MPNH28  MPNH31  MPNH29  MPNH30  MPNH32  MPNH33  MPNH34  MPNH35  MPNH39  MPNH40  MPNH84  MPNH85  MPNH38  MPNH86  MPNH87  MPNH88  MPNH89  MPNH90  MPNH91  MPNH92  MPNH93  MPNH94
1       0.736848876     0.570331764     0.855212627     0.851024091     0.860134142     0.825433266     0.872329624     0.966239759     0.821966889     0.850104311     0.823470084     0.827708427     0.740343237     0.62246906      0.680357754     0.913355941     0.956806369     0.893926587     0.868970872     0.58229228      0.800531161     0.88825149      0.940786902     0.916415194     0.717169696     0.942103259
2       0.016817316     0.087562666     0.018829798     0.012538123     0.007060914     0.016010203     0.009924941     0.000541482     0.026958241     0.023713728     0.010564658     0.009630592     0.01860202      0.08648562      0.055991099     0.014653268     0.005872006     0.003713377     0.004740235     0.053948144     0.014146601     0.00396362      0.001845659     0.004678195     0.014513445     0.002323289
4       0.050126066     0.081614528     0.042585704     0.01527271      0.016063973     0.01575512      0.012095088     0.005061682     0.022535211     0.000907638     0.01004223      0.000522481     0.00730365      0.060888325     0.080674427     0.022959898     0.000700938     0.008518923     0.080249923     0.008721273     0.05404568      0.010382127     0.003810744     0.006067283     0.05177917      0.006062026

Thanks! --Fiona

[Charlie Xia]

Most likely your data has problem. Did you run check_data?

[Fiona Whelan]

No, because I didn't know about it. Is there documentation that I'm missing? I've read the readme and the wiki which only make mention of lsa_compute and lsa_query, unless I'm mistaken.

[Charlie Xia]

Try 'check_data -h'.

[Fiona Whelan]

But as a user, how would I be able to troubleshoot these types of issues myself? i.e. Is there documentation somewhere of all the available scripts as part of eLSA?

[Charlie Xia]

These are mostly experimental and debugging scripts. I will try to add their usages to the wiki. I am preoccupied with other research now but there is always a need to build a good documentation, which I wish some user like you, can help me with.

But anyway, thanks for the suggestions!

[Fiona Whelan]

Good documentation brings users! ;) But I totally understand- writing the documentation is the least fun aspect of writing software. For now, even a list of all available scripts and a one sentence explanation on the wiki would be useful. From there, most users can figure out that -h will give them the information they need. Thanks for your help!

[Charlie Xia]

I totally agree. I am linking this issue to FAQ. Thanks again.