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hello cole and epi,
i have made some comparisons of FPKM values (calculated from count data, not with cufflinks) with corresponding microarray data regarding gene length, and found some interesting details.
it is true that FPKM values from genes with length below 500 bp correlate much less with expression values derived from microarrays, but the differences between tissues (i.e. normal vs. cancer) from small genes correlated even better (NGS vs microarray) than the differences from larger genes (interestingly, the correlations go continuos down. see figure).
and in most study designs, the differences from two conditions are important, not the absolute expression values. therefore, i would not exclude small genes from statistical analysis!
in green and blue are the correlations of lg2_FPKM values from each 12 normal and 12 cancer tissues with corresponding lg2_microarray_expression values from 26 normal and 26 cancer tissues. in red the correlations of the differences (lg2_FPKM_NORMAL - lg2_FPKM_CANCER vs. lg2_microarray_NORMAL - lg2_microarray_CANCER) are shown. on the x-axis genes are grouped according gene length (and the number of genes in each bin are shown), e.g. 190 genes are below 500 bp length.
hello cole and epi,
i have made some comparisons of FPKM values (calculated from count data, not with cufflinks) with corresponding microarray data regarding gene length, and found some interesting details.
it is true that FPKM values from genes with length below 500 bp correlate much less with expression values derived from microarrays, but the differences between tissues (i.e. normal vs. cancer) from small genes correlated even better (NGS vs microarray) than the differences from larger genes (interestingly, the correlations go continuos down. see figure).
and in most study designs, the differences from two conditions are important, not the absolute expression values. therefore, i would not exclude small genes from statistical analysis!
in green and blue are the correlations of lg2_FPKM values from each 12 normal and 12 cancer tissues with corresponding lg2_microarray_expression values from 26 normal and 26 cancer tissues. in red the correlations of the differences (lg2_FPKM_NORMAL - lg2_FPKM_CANCER vs. lg2_microarray_NORMAL - lg2_microarray_CANCER) are shown. on the x-axis genes are grouped according gene length (and the number of genes in each bin are shown), e.g. 190 genes are below 500 bp length.
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