[jp.]

Hi
May please someone check my attached cuff_diff results. I have problem with high error bar and low FPKM value. Is there something wrong with sequencing or its a cufflinks problem?
Second, there are only few genes in either samples (not in all) with 0 FPKM value; for example, control 3840.28 FPKM and treated 0 FPKM with Log2_fold_change=Inf. Attached File 0_FPKM.png Expression bar plot indicates high fold expression ? Can I ignore this one which seems significant ?

Thank you very much

[aguffanti]

Cuffllinks variance, gene expression level and ifferential expression

Hello ! which kind of sequencing was that - fragment or paired ends ? it changes a lot

You have to look at the *count.tracking files and examine the count variance values

There are instances (especially with fragment sequencing) for which the count variance is far greater than the counts - actually I would like to know from Cole wether this is somewhat expected

Here is an example (see the values for q2), with the associated gene expression reported below - looks like for q2 a FPKM of 0 is calculated due to the enormous variance, am I right ?

tracking_id q1_count q1_count_variance q1_count_uncertainty_var q1_count_dispersion_var q1_status q2_count q2_count_variance q2_count_uncertainty_var q2_count_dispersion_var q2_status

GAPDH 308519 40753000 0 308519 OK 207559 10265500000 0 10265500000 OK


test_id gene locus status MCF7 MCFS MCF7+MCFS log2(fold_change) test_stat p_value q_value significant

NM_001256799 GAPDH chr12:6643584-6647537 OK 11.25 0.00 11.25 =-inf nan 0.00005 0.0142079 yes

I am running software versions as follows on Color Space reads (so I have to stick to the old bowtie..)

bowtie version 1.0.0
TopHat v2.0.9
cufflinks v2.1.1

Thanks in advance for any feedback,

Alessandro