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  • #46
    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

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    Last edited by jp.; 07-24-2013, 10:49 PM. Reason: adding info

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    • #47
      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

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