I am a working with DESeq2 (version 1.22.2) on R (version 3.5.3) to analyze my data from RNA sequencing.
I did some tests last week and I had no trouble but this week, for the real analysis, I have a problem.
Coldata table looks like :
> target_OMvsYM label condition taille 1 OM_E1 OM 409 2 OM_E2 OM 519 3 OM_E3 OM 906 4 OM_E4 OM 1836 5 OM_E5 OM 1922 6 OM_E6 OM 2063 7 YM_E1 YM 603 8 YM_E2 YM 834 9 YM_E3 YM 1094 10 YM_E4 YM 1313 11 YM_E5 YM 2643
I have 6 replicates for OM group and 5 replicates for YM group. I am using a second factor which is numeric (taille). I checked that colData labels and colnames of countData are the same
> all(rownames(target_OMvsYM$label) == colnames(counts_ICM_OMvsYM))  TRUE
Then I run my analysis:
dds_ICM_OMvsYM <- DESeqDataSetFromMatrix(countData = counts_ICM_OMvsYM, colData = target_OMvsYM, design= ~ condition + taille) dds_ICM_OMvsYM$condition <- relevel(dds_ICM_OMvsYM$condition, ref = "YM") dds_ICM_OMvsYM<-DESeq(dds_ICM_OMvsYM)
My problem is at this step.
Last week, when I used resultsname, the good name was
but this week I have this resultsname :
> resultsNames(dds_ICM_OMvsYM)  "Intercept" "condition1" "taille"
Why don't I have the same name as last week? Is my DESeq2 analysis good ? I tried to find the answer but I do not know where is the problem.
Thank you for your help !