Hi Simon (and others),
Quick question about DESeq. So far it looks like a nice approach! But it was giving me some somewhat strange (although possible reasonable) numbers...so I wanted to check....
Sometimes the values estimated for baseMeanA and baseMeanB differ in the direction and the extent of change from the original raw counts. Is this expected? These baseMeans are meant to be 'corrected' estimates of read counts for the conditions in question? If I am getting such differences between the raw read counts and the baseMeans, is this simply a reflection of the strength of the dataset (I am running without biological reps). If so, thats fine (I think). But just making sure all is well..
For example...
Is this normal?
Quick question about DESeq. So far it looks like a nice approach! But it was giving me some somewhat strange (although possible reasonable) numbers...so I wanted to check....
Sometimes the values estimated for baseMeanA and baseMeanB differ in the direction and the extent of change from the original raw counts. Is this expected? These baseMeans are meant to be 'corrected' estimates of read counts for the conditions in question? If I am getting such differences between the raw read counts and the baseMeans, is this simply a reflection of the strength of the dataset (I am running without biological reps). If so, thats fine (I think). But just making sure all is well..
For example...
Code:
Counts_Novel Counts_Familiar DESeq-id DESeq-baseMean DESeq-baseMeanA DESeq-baseMeanB DESeq-foldChange 141 139 28 140.176915 133.0658319 147.2879981 1.106880677 143 136 30 139.5312055 134.9532905 144.1091204 1.067844436
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