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Dear Alexandre,<br>
<br>
Many thanks for your bug report and I was able to reproduce it. In
fact, it seems to me that we should ignore the warning in that case.
<br>
<br>
It happens that the matrix computed by seqsubm is not exactly
symmetric due to very small to rounding errors. The differences
should be extremely low (something like 1e-16). You may check that
by using the following code:<br>
<br>
subm - t(subm)<br>
<br>
The resulting matrix should contains only zero or extremely low
values.<br>
<br>
Hope this helps<br>
Matthias<br>
<br>
<br>
Le 15.04.2011 17:29, Alexandre Pollien a écrit :
<blockquote cite="mid:4DA8645A.6020903@unil.ch" type="cite">Hello,
<br>
<br>
When I use seqsubm, now I get this message:
<br>
<br>
<blockquote type="cite"> contact.om<- </blockquote>
seqdist(contact.seq,method="OM",indel=2,sm=cout,with.missing=FALSE,
full.matrix=TRUE)
<br>
[>] 5764 sequences with 9 distinct events/states
<br>
[>] 496 distinct sequences
<br>
[>] min/max sequence length: 1/12
<br>
[>] computing distances using OM metric
<br>
[>] total time: 1.25 secs
<br>
Message d'avis :
<br>
The substitution cost matrix is not symmetric.
<br>
<br>
cout is computed with seqsubm (method="TRATE")
<br>
<br>
<br>
A surprising aspect is that it is not systematic (3 / 4)
<br>
<br>
I thought of a problem of missing value
<br>
<br>
<br>
Another amazing prompt is that seqdef shows this message:
<br>
<blockquote type="cite"> contact.seq <- seqdef(contact, 2:15,
states = contact.shortlab,labels </blockquote>
= contact.lab)
<br>
[>] found missing values ('NA') in sequence data
<br>
<br>
...even when there is no missing in my data! (How can I seethe
sequence containing the missing data?)
<br>
<br>
<br>
Does anyone have a idea?
<br>
<br>
Thank you very much
<br>
<br>
Best regards and good weekend
<br>
<br>
Alexandre
<br>
<br>
<br>
<br>
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