From: Genome-wide transcription profiling of human sepsis: a systematic review
Prucha[14] | Ramilo[17] | Tang-2[18] | Talwar[8] | Payen[19] | Pachot[22] | Prabhakar[9] | Calvano[10] | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Data acquisition | ||||||||||||
Tissue homogeneity of target samples | Low | High | High | High | High | High | High | Low | High | Low | Low | High |
Experiments follow miame criteria¶ | Yes | Yes | Yes | Yes | Not clear | Yes | Not clear | Not clear | Not clear | Not clear | Yes | Not clear |
Reporting of normalization method | No | Yes | Yes | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes |
Analytical issues | ||||||||||||
Method for gene selection | t test | t test | Non-parametric test | t test | ANOVA | t test | Multiple | Not clear | Not clear | SAM | ANOVA and fold change | Non-parametric test |
Issue of variance estimation addressed | No | Yes | No | Yes | No | No | Not clear | Not clear | Not clear | Yes | No | No |
Comparison to other diagnostic markers | No | No | No | No | No | NA | Yes | Yes | No | No | No | Yes |
Correction for multiple testing | Yes | Yes | Yes | Yes | Yes | NA | Yes | Yes | No | Yes | Yes | Yes |
Reporting of classifier performance | No | Yes | No | Yes | NA | NA | No | Yes | NA | NA | Yes | NA |
Reporting of prediction accuracy | No | Yes | Yes | Yes | NA | NA | Yes | Yes | NA | NA | Yes | NA |
Validation of data | ||||||||||||
Cross validation of signature genes | No | Yes | Yes | Yes | No | No | Yes | Yes | NA | No | Yes | Yes |
External validation in independent samples | No | Yes | Yes | Yes | No | No | Yes | Yes | NA | Yes | Yes | No |
Ratio of test/training sample size | NA | 1.14 | 2.00 | 1.00 | NA | NA | 0.50 | 0.23 | NA | 0.75 | 0.77 | NA |
Adjustment for confounders | No | Yes | Yes | No | NA | NA | No | No | No | NA | Yes | Yes |
Raw data made publicly available | No | Yes | Yes | Yes | Yes | Yes | No | No | No | No | Yes | No |
PCR validation | Yes | No | Yes | Yes | Yes | Yes | Yes | Yes | Yes | No | No | Yes |