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Rarefaction analyses of both unfiltered datasets revealed that the biogas-producing community is covered much deeper by the Titanium than by the GS FLX sequences (Figure 7).
Results using a second analytical approach in which the total (unfiltered) datasets were each assembled into contigs, queried and hits retrieved based on E-value <10−4 detected higher frequencies of hits in each fraction (Table 3), however both approaches revealed similar proportions of Gymny elements in the genomic fractions relative to one another (Pearson's correlation, r = 0.97).
Both the filtered and the unfiltered datasets only included interactions reported as physical, thereby excluding genetic interactions.
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Figure 2A shows the frequency distribution of the Log10 values of the NAF corrected for number of tryptic peptides for the 946 proteins in the initial unfiltered dataset from stromal samples.
Two filtered datasets were produced alongside an unfiltered dataset; these excluded reactions reported less than either twice or three times in the literature.
Analysis C, the unfiltered dataset, is defined as all of the genes on the microarray that had data present for 90% of the arrays.
The results using the unfiltered dataset (dataset I), which resulted in the inflation of variance, are provided in Additional file 3. Genes that have evolved under positive selection were searched with the model-based likelihood ratio test [ 40].
We measured the search space reduction (see Supplementary Fig. 4 for results for the first 20 TIGRFAM families) and the total runtimes of PSfamSearch and compared them with hmmsearch operating on the unfiltered dataset.
We shared our raw data exactly to emphasize the point of how noisy this unconstrained, virtually unfiltered dataset was, and how important it was to account for this variability.
In contrast, we err on the side of false negatives by using strict 1) multi-species criteria and 2) gene-family specific domain models to cast a highly restrictive "lens" on Krogan et al's massive unfiltered dataset.
In the primary (unfiltered) dataset, distribution of correlation coefficients for β2 log2MRIPA was distinctly bimodal, with a major mode occurring between 0 and −0.5, and a minor mode occurring between 0.25 and 0.75.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com