I'm trying to reproduce an old analysis I did using the bioc package limma. I've cloned the git repo and I do see limma versions that are part of bioc releases, but I don't see versions 3.43.4 or 3.43.5 there. I also don't see these versions in the cran archive. And google hasn't produced any other leads.
Does someone know how I can download these versions?
The limma versions that you mention were developmental versions rather than release versions of limma and you should not be using those for analyses unless you are a Bioconductor developer yourself. Anyway, there have been no changes to limma since those versions that would change the results of a standard DE analysis with a full-rank design matrix and estimable coefficients.
As well as the git log, you can see a human-friendly summary of each change for every version of limma from limma::changeLog(). If you only need to see a summary of the changes corresponding to each Bioconductor release, then:
Setting aside the need for an exact version of limma, it's simple enough to get whichever one you want.
## After having done
git clone https://git.bioconductor.org/packages/limma
## and going into the limma directory
$ git log | grep -n 3.43.4
539: 16 Feb 2020: limma 3.43.4
7860:Date: Wed May 27 23:43:46 2009 +0000
## so we want to be around line 539
$ git log | sed -n '530,540p'
the presence of non-estimable coefficients sometimes caused the
cov.coefficient matrix to be subsetted incorrectly; that is now
fixed. Subsetting zero columns is now allowed even when F-statistics
commit fb2ce173d94fee80707ba421876c85530f2ad112 <------------------------ the important thing
Author: Gordon Smyth <firstname.lastname@example.org>
Date: Sun Feb 16 21:16:40 2020 +1100
16 Feb 2020: limma 3.43.4
$ git checkout fb2ce173d94fee80707ba421876c85530f2ad112
Note: switching to 'fb2ce173d94fee80707ba421876c85530f2ad112'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at fb2ce17 16 Feb 2020: limma 3.43.4
And now you can install and do your analysis.
However, there have been 54 commits to limma in the intervening period, and presumably they weren't made for arbitrary reasons. One could argue that using the current release version of limma is materially better than using an old version, even if some of the results change. OTOH, I work in a core, and have people ask me to re-run old analyses to add new contrasts or whatever, and they tend to be less than happy if I do so and some of their existing gene lists change, so I get not wanting things to change...