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Hi All!
I have encountered what i believe to be a problem (may not be a problem though) with the output data i have generated using CuffDiff. In my experiment i am comparing transcript expression in a condition (in this case a head and neck cancer cell line) vs a control (in this case normal human keratinocytes), unfortunately i do not have replicates for each of these conditions.
When analyzing the results (from transcript differential expression testing output) i have found two significant changes where FPKM values can be found for both conditions (i.e the transcript is expressed in the both samples) but i also have a large amount of significant changes (around 150) where FPKM values are present for one condition but not for the other (i.e transcript is expressed in one sample but not the other).
I was unsure whether this is something commonly observed in these sort of analyses, whether the lack of replicates for each condition influences this or whether i may have made some mistake during the pipeline (i used the TopHat - Cufflinks - Cuffmerge - CuffDiff pipeline).
I have encountered what i believe to be a problem (may not be a problem though) with the output data i have generated using CuffDiff. In my experiment i am comparing transcript expression in a condition (in this case a head and neck cancer cell line) vs a control (in this case normal human keratinocytes), unfortunately i do not have replicates for each of these conditions.
When analyzing the results (from transcript differential expression testing output) i have found two significant changes where FPKM values can be found for both conditions (i.e the transcript is expressed in the both samples) but i also have a large amount of significant changes (around 150) where FPKM values are present for one condition but not for the other (i.e transcript is expressed in one sample but not the other).
I was unsure whether this is something commonly observed in these sort of analyses, whether the lack of replicates for each condition influences this or whether i may have made some mistake during the pipeline (i used the TopHat - Cufflinks - Cuffmerge - CuffDiff pipeline).