comparing samples with varying no. of reads for differential expression

[harshinamdar]

can two samples with different number of reads be compared using cufflinks package ? say I have sample A with 6 million paired end reads and sample B with 8 million paired end reads; can they be compared using cufflinks for differential expression?

[kmcarr]

Cufflinks reports expression as FPKM, which stands for Fragments Per Kilobase of exon model per Million reads mapped. That last bit "per million reads mapped" is meant to adjust the expression measurement for sample size.