Hi, I'm looking at transcription in WT and K/O ES cells of a particular gene - I have three biological replicates of each genotype - two of each are from 129 mouse ES cells and the other one of each genotype is from a black 6 mouse ES cell.
I'm slightly confused by a figure I produced using DESeq which has PC1 and PC2 on it's axes - I understand that simmilar cell types (though not sure how DESeq has calculated 'simmilarity' in this case?) are supposed to cluster together, but I have a pair of WT and KO cells that seem to cluster closer together - could these be the black6 ES cells?
Are strain differences commonly associated with transciptional differences large enough to produce this kind of effect? Could anyone explain this figure to me? I've attached another version which I ran with only 129 samples (it only has four points) - it is also not clear from the DESeq mannual how to label samples when producing these blots.
Would appreciate any advice
Thanks
Alex
I'm slightly confused by a figure I produced using DESeq which has PC1 and PC2 on it's axes - I understand that simmilar cell types (though not sure how DESeq has calculated 'simmilarity' in this case?) are supposed to cluster together, but I have a pair of WT and KO cells that seem to cluster closer together - could these be the black6 ES cells?
Are strain differences commonly associated with transciptional differences large enough to produce this kind of effect? Could anyone explain this figure to me? I've attached another version which I ran with only 129 samples (it only has four points) - it is also not clear from the DESeq mannual how to label samples when producing these blots.
Would appreciate any advice
Thanks
Alex
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