gravatar for andreiareis1987

2 hours ago by

Hi there!

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)


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,

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