I am doing Rnaseq data analysis with yeast samples.
I have the following conditions:A_1, A_200, B_1 and B_200 total of 18 samples and after the filtering the null and getting out the genes that has counts in only one sample, I end up with 6698 genes.
I did a default normalization:
dds<-DESeqDataSetFromMatrix(countData = table, colData = data, design= ~ Cell_Gen) dds<-DESeq(dds)
And i performed the statistical test to found the degs:
results(dds, name=c("Cell_Gen_A_200_vs_A_1"), pAdjustMethod="fdr", lfcThreshold = 1, alpha=0.05)
In this particularly comparison i got several degs but one has counts in only one sample (for the total samples in the specific conditions) :
28A 28C 29A 29C 30A 31A 32A 33A 34A 34C 37A 37C 38C 41A 41C 45C 68C GeneX 0 0 0 0 0 0 0 3680 0 3203 0 0 3710 0 0 0 0
In this case only de sample 33A others samples that end with A dont have counts, so i wonder why this is a deg.
log2FC pvalue padj GeneX 24.445038 7.98e-08 7.61e-05
For others comparisons i got others genes but with same situation... with only counts in one sample.
I will be very much appreciated if anyone clarify me?
All the best,