standOff, and the article is at its publisher via the link below. When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.| relation to other work | claim_relations | how this paper stands to another: agrees, contradicts, extends, qualifies |
| claim type | claim_type | the shape of the claim: existence, mechanism, method, critique, prediction, null |
| concept | concepts | an idea the paper works with, quoted where the paper uses it |
| content tag | content_tags | a finding, definition, quantity, statistic or variable named in the paper |
| contribution | contribution | what the paper claims to add |
| control | controls | an experiment run to eliminate a rival explanation |
| limitation | limitations | what the paper says its evidence cannot support |
| mechanism | mechanisms | how the reported effect is said to come about |
| method | method | how the paper produced its evidence |
| object of study | object_of_study | what the paper is about — the thing it investigates |
| phenomenon | phenomenon | the effect or regularity under study |
| research question | research_question | the question the paper sets itself |
| sense | senses | a distinct use of a term, quoted where the paper fixes it |
This record holds no relations between concepts. A layer is empty when the tagger recorded nothing in it — which is not the same as the paper having nothing to record.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | the logarithmic fold change between conditions in RNA-seq, and what to do when the estimate of it is dominated by noise Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | object_of_study | the paper's words | |
| research_question | how to shrink unreliable effect-size estimates without losing the genes whose large effects are real Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | research_question | the paper's words | |
| contribution | a heavy-tailed Cauchy prior that removes the need for filter thresholds and pseudocounts, with lower bias than earlier shrinkage estimators Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | contribution | the paper's words | |
| claim_type | method Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_type | the paper's words | |
| phenomenon | maximum-likelihood effect sizes that blow up when counts are low, producing large estimates that are not differences Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | phenomenon | the paper's words | |
| method | system-or-tool-building Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: system-or-tool-building | method | the paper's words | |
| mechanisms | the estimate is unreliable exactly where the counts are small, so the maximum likelihood LFC has high variance and produces `large estimates not representative of true differences` - the noise appears as a big effect, not as a small one Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[0] | 0.95 | the tagger's words |
| mechanisms | a heavy tail on the prior is what lets shrinkage be aggressive near zero and gentle far from it: the Cauchy pulls in the noise-driven estimates while leaving genuinely large fold changes where they are Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | swapping a Normal prior for a Cauchy gives heavy tails, so small effects are still shrunk while genuinely large ones survive - shrinkage without flattening Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[2] | 0.95 | the tagger's words |
| mechanisms | the prior's scale is fitted by subtracting each estimate's own error variance from its squared value, so the prior learns how much of the observed spread is real Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[3] | 0.95 | the tagger's words |
| mechanisms | the scale is set from a Normal assumption even though the prior itself is Cauchy - the two roles come apart and the authors say the mismatch works in practice Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[4] | 0.9 | the tagger's words |
| limitations | EVERY STANDARD CORRECTION TRADES ONE ERROR FOR THE OPPOSITE ONE: `filtering or application of Normal priors each can have drawbacks, either leading to loss of genes with sufficient signal, or overly aggressive shrinkage of true, large LFCs` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[0] | 0.95 | the tagger's words |
| limitations | and the second-order cost is stated: filtering loses genes with real differences, and `pseudocounts provide a limited solution that must be adapted per dataset` - a correction re-tuned per dataset is a free parameter wearing a method's name Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[1] | 0.95 | the tagger's words |
| limitations | choosing the filter is named as an act of judgement rather than a setting: `Setting the threshold requires careful consideration of which genes may be lost` Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[2] | 0.95 | the tagger's words |
| limitations | if most genes move in the same direction the global normalisation breaks down - and the paper says this defeats EVERY method under comparison, not only theirs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[3] | 0.95 | the tagger's words |
| limitations | that failure is detectable, and the paper names the diagnostics rather than leaving it as a caveat Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[4] | 0.95 | the tagger's words |
| limitations | where the maximum likelihood estimates are not supplied the prior scale falls back to a fixed value rather than being fitted Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[5] | 0.9 | the tagger's words |
| controls | the method is compared against BOTH failure modes rather than against one baseline - filtering, which loses genes, and Normal priors, which over-shrink Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a new estimator that beats the over-shrinking baseline by under-shrinking, or the reverse; the two-sided comparison is what makes 'lower bias while still reducing variance' a claim rather than a trade · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | whether the correction needs a per-dataset parameter Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a method whose performance is really the analyst's tuning - the proposed prior 'avoids the use of filter thresholds or pseudocounts' entirely · outcome: held | controls[1] | 0.95 | the tagger's words |
| controls | whether the approach is tied to the negative-binomial likelihood it was developed on Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a method that works because of one distributional assumption - apeglm 'accepts arbitrary likelihoods, as long as additional parameters are pre-specified' · outcome: held | controls[2] | 0.95 | the tagger's words |
| controls | testing robustness when the assumption of a unimodal symmetric distribution of effects is violated Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the possibility that the method only works when its own prior assumption happens to hold · outcome: held | controls[3] | 0.95 | the tagger's words |
| controls | quantifying the effect of substituting estimated standard errors where the derivation requires known ones, specifically at very low counts Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the possibility that the borrowed estimator breaks exactly where the data are weakest · outcome: held | controls[4] | 0.95 | the tagger's words |
| controls | trying an alternative posterior approximation by integrating over a fine grid instead of the Laplace method Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the possibility that the chosen approximation was adopted without a competitor · outcome: failed | controls[5] | 0.95 | the tagger's words |
| concepts | logarithmic fold change Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: logarithmic fold change | concepts[0] | 0.95 | the paper's words |
| concepts | pseudocounts Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: pseudocounts | concepts[1] | 0.95 | the paper's words |
| concepts | shrinkage estimator Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: shrinkage estimator | concepts[2] | 0.95 | the paper's words |
| concepts | Cauchy prior Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Cauchy prior | concepts[3] | 0.95 | the paper's words |
| concepts | local false sign rate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: local false sign rate | concepts[4] | 0.95 | the paper's words |
| concepts | Laplace approximation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Laplace approximation | concepts[5] | 0.95 | the paper's words |
| concepts | empirical Bayes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: empirical Bayes | concepts[6] | 0.95 | the paper's words |
| concepts | maximum a posteriori Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: maximum a posteriori | concepts[7] | 0.9 | the paper's words |
| senses | logarithmic fold change - AS ESTIMATED, NOT AS DEFINED. The definition is a ratio of average expression between conditions; the estimate at low counts is `large ... not representative of true differences`. THE SAME SYMBOL NAMES A QUANTITY AND A NUMBER THAT DOES NOT MEASURE IT Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[0] | 0.95 | the tagger's words |
| senses | shrinkage - the family of corrections, and this paper's point is that the family members fail in OPPOSITE directions: a filter loses true signal, a Normal prior flattens true large effects. WHICH ERROR YOU GET IS A CHOICE, AND USUALLY AN UNEXAMINED ONE Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[1] | 0.95 | the tagger's words |
| senses | pseudocount - a correction that `must be adapted per dataset`. The paper's remedy is to remove the parameter rather than to tune it, which is the same move a field makes when it replaces an inferred name with a measured one Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[2] | 0.95 | the tagger's words |
| claim_relations | critiques → count filtering as practised in edgeR and limma-voom, which removes genes before analysis and can lose those with sufficient signal Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | critiques → DESeq2's adaptive Normal prior, which shrinks true large fold changes too aggressively Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[1] | 0.95 | the tagger's words |
| claim_relations | extends → the empirical Bayes shrinkage tradition itself - the method is offered as a replacement for the prior, not for the framework Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[2] | 0.95 | the tagger's words |
| content_tags | filtering loses genes with sufficient signal, while Normal priors over-shrink true large LFCs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[0] | 0.95 | the tagger's words |
| content_tags | pseudocounts provide only a limited solution that must be adapted to each dataset Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[1] | 0.95 | the tagger's words |
| content_tags | setting the filter threshold requires careful thought about which genes may be lost Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[2] | 0.95 | the tagger's words |
| content_tags | at low or highly variable counts the maximum-likelihood LFC has high variance, giving large estimates not representative of true differences Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[3] | 0.95 | the tagger's words |
| content_tags | the proposed heavy-tailed Cauchy prior avoids filter thresholds and pseudocounts Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[4] | 0.95 | the tagger's words |
| content_tags | the Laplace approximation was consistently more accurate than numerical integration over a grid Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[5] | 0.95 | the tagger's words |
| content_tags | the resulting scale estimate is only slightly biased even at very low counts Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[6] | 0.95 | the tagger's words |
| content_tags | shrinkage improves the ranking of genes by effect size relative to methods that do not shrink at all Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[7] | 0.95 | the tagger's words |
| content_tags | the difference between conditions, defined as the log ratio of average expression levels Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: logarithmic fold change | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | the local false sign rate given as a two-case posterior probability keyed on the sign of the MAP estimate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: local false sign rate | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | maximum likelihood Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: maximum likelihood | content_tags.statistics[0] | 0.95 | the tagger's words |
| content_tags | variance Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: variance | content_tags.statistics[1] | 0.95 | the tagger's words |
| content_tags | posterior SD Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: posterior SD | content_tags.statistics[2] | 0.85 | the tagger's words |
| content_tags | library size Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: library size | content_tags.variables[0] | 0.95 | the tagger's words |
| content_tags | runtimes for the pipeline on a ten-thousand-gene simulation - dispersion and MLE fitting, Normal-prior shrinkage, Cauchy-prior shrinkage, and MAP-only Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[0] | 0.95 | the tagger's words |
Tags that could not be placed in the text:
What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.