I  am having some trouble  with DEseq analysis. While doing certain
comparison i get adjusted pvalue of 1 or 0.9 . And the summary looks like
following .Other comparison of the same matrix works fine. I do have replicates and there fore that is not the issue. Stage 11 comparison with all other stages works but when i  start doing stage 15 to 18 it gives p value 1.  

> summary(DEcellresults)

out of 141995 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up)     : 0, 0%
LFC < 0 (down)   : 0, 0%
outliers [1]     : 0, 0%
low counts [2]   : 0, 0%
(mean count < 0.2)

The first few lines  matrix looks like :
stage11AC    stage11AC_R    stage15PLE    stage15PLE_R    stage18PLE    stage18PLE_R    stage21PLE    stage21PLE_R
Chr01:49237-49304    1    3    6    59    2    17    7    13
Chr01:129220-129302    2    0    5    2    2    27    7    5
Chr01:199946-200029    3    11    10    22    17    28    13    12
Chr01:225229-225351    8    25    9    64    10    29    28    20
Chr01:281568-281632    13    0    13    20    12    34    8    15
Chr01:290493-290585    4    14    17    4    9    11    11    14
Chr01:315271-315349    0    3    3    26    8    21    7    8
Chr01:386958-387030    6    3    1    27    2    6    11    8
Chr01:444075-444146    0    0    5    29    6    1    18    8

Do you have any suggestion on how to solve this.

Thanks in advance

best

Ann

This just means that there were no significant genes, either because there is no difference across treatment, or more likely, that the experiment was underpowered (often too few samples) to detect differential expression above the within-group variance.

The fact that the adjusted p-values are equal to 1 or have similar high value is a consequence of the correction method of Benjamini Hochberg. See this previous post of mine:

C: adj.P metod = \"BH\" many exact the same value

Ann: Have you done diagnostic plots for quality (heatmap, sample clustering, PCA of samples, pairwise scatterplots) to check that the replicates really look like replicates and the different conditions cluster as expected?