Hey folks
I'm running CuffDiff from the release 0.9.2, for RNAseq. I use it with tophat, and Reference annotation for human data. Here's the simple running command:
There are few points of concern
first: over 90% of the genes with "status = OK" have "Significant = yes" which is kinda not so nice.
second: that there are so many genes with very low FPKM that are among the significant ones, which can also lead to fold changes like: 1.7977e+308 !
and third: There are genes with large FPKMs that have not been tested (status = NOTEST) , here's some sample, from the file "genes_expr.diff", with a "NOTEST gene with hight FPKM, and two low FPKM genes with test status "OK":
Does somebody have some idea? :-/
thanks
pej
I'm running CuffDiff from the release 0.9.2, for RNAseq. I use it with tophat, and Reference annotation for human data. Here's the simple running command:
Code:
cuffdiff --FDR 0.01 -N hg18_annotation01.gtf accepted_hits1.bam accepted_hits2.bam
There are few points of concern
first: over 90% of the genes with "status = OK" have "Significant = yes" which is kinda not so nice.
second: that there are so many genes with very low FPKM that are among the significant ones, which can also lead to fold changes like: 1.7977e+308 !
and third: There are genes with large FPKMs that have not been tested (status = NOTEST) , here's some sample, from the file "genes_expr.diff", with a "NOTEST gene with hight FPKM, and two low FPKM genes with test status "OK":
Code:
ttest_id status value_1 value_2 ln(fold_change) test_stat p_value significant NR_036659 NOTEST 1119.85 6601.74 1.774 -54.911 0 no NM_001130440 OK 5.6E-09 5.7E-09 0.030 -1.744 0.081 no NM_001001977 OK 9.7E-09 1.2E-08 0.227 -18.416 0 yes
thanks
pej
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