User: Marc Carlson

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Marc Carlson7.2k
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Posts by Marc Carlson

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Answer: A: problem with makeOrgPackageFromNCBI when making an annotation package
... Hi Shisheng, Can I ask why it is that you want to call this function instead of just using the OrgDb objects that have been pre-built and loaded into AnnotationHub?    Marc ...
written 15 months ago by Marc Carlson7.2k
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Answer: A: Tools for GO term enrichment in prokaryotes
... Hi, So the tricky part here is that you are looking at a non-model prokayote and you need GO to gene mappings to do the kind of analysis that you propose.  Where could you find these?  Well that depends on just how 'non-model' your organism is...  If your organism doesn't have assigned gene IDs and ...
written 2.3 years ago by Marc Carlson7.2k
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Answer: A: Find human SNP orthologous flanking sequence
... Hi Juan, There are several possible answers to this depending on exactly what you are starting with and what you want to find at the end.  I will make one guess about what you wanted here but others may have other ideas.  If your starting point is a range then you could do this: First lets assume ...
written 2.3 years ago by Marc Carlson7.2k
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Answer: A: makeTxdbfromUCSC Warning message
... This warning is really just telling you something about the source data and not about the TxDb.  Since it is expected that a cds length would be divisible by three, the code checks for that and reports to you whenever this doesn't happen.  You can decide what you want to do about it (if anything).   ...
written 2.3 years ago by Marc Carlson7.2k
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Answer: A: How to create an output file with sequence ID's from multiple BLAST result using
... Hi Mathilde, In your case it sounds like you might just want to use the argument to the blastSequences function called 'as' and set it to 'data.frame'.  This can return a lot of other data back to you about what exactly your sequence aligns to.  So just modifying the example from the man page here ...
written 2.3 years ago by Marc Carlson7.2k
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Answer: A: Bug: mappedkeys(ath1121501ACCNUM) returns character(0)
... OK.  I have just pushed repaired packages online for these two chip packages.  Look for version 3.1.4 to appear within the next day or so on the website.    Marc ...
written 2.4 years ago by Marc Carlson7.2k
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Answer: A: Bug: mappedkeys(ath1121501ACCNUM) returns character(0)
... Wow.  Thanks for this bug report.  I have code that checks for these things but apparently the probes for arabidopsis have slipped past my current dragnet for missing fields. I will find out what went wrong and fix the package.  And then I will update the dragnet so this kind of problem doesn't hap ...
written 2.4 years ago by Marc Carlson7.2k
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Answer: A: AnnotationForge/SQLForge: how to add data after creating the new package
... Hi Sylvain, So you have generated an annotation package and installed it into your library.  Why do you now want to insert these other data into the database for your annotation package?  Do you really need to do that?  Because there are many immediate downsides to that approach, and there are othe ...
written 2.4 years ago by Marc Carlson7.2k
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Comment: C: AnnotationDbi packages missing in current release
... And another good tip that might help is to look at the posting guide.  Which you can see here: http://bioconductor.org/help/support/posting-guide/ ...
written 2.4 years ago by Marc Carlson7.2k
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Answer: A: pd.huex.1.0.st.v2 package doubt
... Hi Elena, So we have been digging into this since you brought it to our attention, and it seems that the set of Affy based annotations that were recommended by Affy as the most recent at the time when the last batch of annotation packages were made (IOW all of the packages based on Affys na34 relea ...
written 2.5 years ago by Marc Carlson7.2k

Latest awards to Marc Carlson

Scholar 2.2 years ago, created an answer that has been accepted. For A: Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 2.8 years ago, created an answer that has been accepted. For A: Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Autobiographer 3.2 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.2 years ago, created 100 posts.

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