Comments for The Bowman Lab

Comment on Tutorial: Analysis with paprica by Nathan

Nathan — Sun, 14 Jan 2024 23:34:22 +0000

Hi Jeff,

Great program, and I’m excited to see my results. I successfully ran my own samples, but when I try to run the combine_results code, I end up with an error — specifically, it flags a nan value and throws a KeyError, which should be handled by the exception line in the code (see the copied source code below, line 256). However, it throws another error on line 248: “ValueError: cannot reindex on an axis with duplicate labels.” Any ideas on what could be going wrong? I didn’t want to try debug the source code without seeing if you had any ideas first. Thanks!

try:
unique_edge_abund.loc[seq, temp_unique.loc[seq, ‘global_edge_num’]] += temp_unique.loc[seq, ‘abundance_corrected’]
except KeyError:
unique_edge_abund.loc[seq, temp_unique.loc[seq, ‘global_edge_num’]] = temp_unique.loc[seq, ‘abundance_corrected’]

Comment on Tutorial: Self Organizing Maps in R by Matt

Matt — Mon, 08 Jan 2024 17:00:46 +0000

First, super-helpful, and I really appreciate having this page and code to work through, as I am researching this.

One question on `clusterMeanDist()`… maybe it doesn’t matter, but when computing cluster means with `mean(temp.dist)`, that is taking the means of a symmetric matrix with a diagonal of zeros. Would it be better to take the means of the unique pairs of distances and do not include the zero self-distances? Or does the general trend hold anyway? I was thinking it might matter if the clusters are very imbalanced…

Comment on Phylogenetic placement re-re-visited by Francesco

Francesco — Tue, 26 Sep 2023 09:53:20 +0000

P.S: I forgot to mention that the posted link for the 16S_bacteria.cm file apparently does no works

Comment on Phylogenetic placement re-re-visited by Francesco

Francesco — Tue, 26 Sep 2023 09:43:48 +0000

Hi Jeff, thank you very much for this tutorial, it is amazing. Only, I am quite new with this kind of analysis and I am not sure about the “Pfam 16S_bacteria.cm” file, where can I found and download it? In advance, thank you very much for your help. Fra

Comment on Parsing blast xml output by Ben

Ben — Wed, 30 Aug 2023 06:31:01 +0000

Since I am reading this today, some might be tempted to use this in 2023: be careful when using .strip(foo) and .rstrip(bar)

They do not remove the foo and bar prefixes/suffixes, they would remove from the ends of the string (or only the tail when using rstrip) every character belonging in the set ‘foo’ or ‘bar’.

Example :
”’
>>> s = “id_seed”
>>> s.strip(“”).strip(“ 'seed'
'''

…and the "id_" is lost!

Comment on New postdoctoral research opportunity! by Jeff

Jeff — Thu, 06 Jul 2023 13:35:58 +0000

Position has been filled!

Comment on Weighted Gene Correlation Network Analysis (WGCNA) Applied to Microbial Communities by Dinesh

Dinesh — Thu, 25 Aug 2022 08:33:24 +0000

Hi there,
Thanks a lot. It would be great if you could share code for cytoscape export or sample .csv files (edge and node).

Regards,
Dinesh

Comment on Tutorial: Self Organizing Maps in R by Dominik

Dominik — Wed, 16 Feb 2022 13:26:08 +0000

In reply to David Covell.

Hello,
as the help site for pbdMPI (?pbdMPI) says, you need some sort of MPI-Library installed. For me, Windows 10, the current version of MS-MPI solved the loading problem and the code runs fine. If your OS differs, then you need to search for a compatible library.

Cheers

Comment on Tutorial: Self Organizing Maps in R by Jeff

Jeff — Wed, 09 Feb 2022 16:46:11 +0000

In reply to Ananya Ramesh. Thanks for the comment Ananya. That's a package question so I encourage you to reach out to the pmclust and pdbMPI developers if there's an issue installing those packages.

Comment on Tutorial: Self Organizing Maps in R by Ananya Ramesh

Ananya Ramesh — Tue, 08 Feb 2022 12:07:28 +0000

In reply to Jeff. Thanks for the tutorial, but I am also getting the same error as David. Can you help in fixing it?