how to select best significant

Question

[haribioinfo05]

how to select best significant in t-test value?

ID              adj.P.Val    P.Value     t           B           logFC       Gene.symbol    Gene.title
ILMN_1745607    3.50E-57     7.40E-62    38.6646     128.3397    8.106586    A2M            alpha-2-macroglobulin
ILMN_1752755    4.38E-44     1.85E-48    27.56745    99.19733    7.387721    VWF            von Willebrand factor
ILMN_2157441    8.54E-43     6.70E-47    26.46402    95.74092    7.017251    HLA-DRA        major histocompatibility complex, class II, DR alpha
ILMN_1709162    8.54E-43     7.22E-47    -26.4416    95.66943    -3.17902    SHCBP1         SHC SH2-domain binding protein 1
ILMN_1761733    9.81E-43     1.04E-46    26.33227    95.32021    6.422425    HLA-DMB        major histocompatibility complex, class II, DM beta
ILMN_3250257    2.40E-42     3.04E-46    26.00918    94.28114    4.908232    ACVRL1         activin A receptor type II-like 1
ILMN_1704730    6.44E-42     9.53E-46    25.66985    93.17846    6.000549    CD93           CD93 molecule
ILMN_1693826    5.49E-40     9.28E-44    24.34132    88.74547    5.449931    HAVCR2         hepatitis A virus cellular receptor 2
ILMN_2141482    7.72E-40     1.47E-43    24.21095    88.30028    5.984509    SERPINF1       serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1
ILMN_1778977    1.07E-39     2.25E-43    24.08983    87.88503    6.99495     TYROBP         TYRO protein tyrosine kinase binding protein
ILMN_1772218    1.30E-39     3.02E-43    24.00719    87.60076    7.480757    HLA-DPA1       major histocompatibility complex, class II, DP alpha 1
ILMN_2379644    2.52E-39     6.39E-43    23.79661    86.87301    7.209751    CD74           CD74 molecule, major histocompatibility complex, class II invariant chain
ILMN_1727045    1.47E-38     4.04E-42    23.28435    85.08197    4.244664    RASGRP3        RAS guanyl releasing protein 3 (calcium and DAG-regulated)
ILMN_1748473    3.13E-38     9.26E-42    23.05602    84.27407    5.459673    GIMAP4         GTPase, IMAP family member 4
ILMN_1879857    3.57E-38     1.13E-41    -23.0011    84.07903    -1.86797          
ILMN_1736567    6.16E-38     2.08E-41    22.83467    83.48521    7.592408    CD74           CD74 molecule, major histocompatibility complex, class II invariant chain

[Ram]

Hari, your last question was phrased better, giving us more details on your experiment and your requirements. You are now slipping into your old habits of context-less copy-paste, which is not good. Multiple posts also work against you. Do not repeat this, please.

Answer 1

[Whoknows]

Hi

You can consider those genes with fold change -1.5 to +1.5 or -2 to +2, to convert Logfc use power 2

Significant genes then will be those with adjPValue / qValue or if you don't have them you must use P-value which below 0.05< , So:

FC : -1.5 to +1.5 or -2 to +2

qValue / adjPvalue / Pvalue : 0.05 or less

[haribioinfo05]

Thank you

Answer 2

[Sean Davis]

The adj.P.Value is likely a false discovery rate (FDR). That has a very nice biological interpretation. If, for example, there are 100 genes with a maximum FDR of 0.1, then 10% of the 100 genes are likely to be false discoveries. From this point-of-view, the FDR has no "accepted" cutoff since a 10% FDR might be totally acceptable for one investigator and study while a 50% FDR (0.5) is acceptable to another. Whether or not one includes fold change as a criterion will vary based on the experimental questions and setup. One criterion that should NOT be used is an unadjusted p-value.