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Question: Help!!! Cuffdiff Log2 Value
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gravatar for 杨继文
6.6 years ago by
杨继文 • 210
杨继文 • 210 wrote:
Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your help. Thanks in advance. Best Jiwen
rna-seq cuffdiff • 4.6k views
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modified 6.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.6 years ago by 杨继文 • 210
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gravatar for Jennifer Hillman Jackson
6.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Jiwen, As far as I know, this is possible. The CuffDiff log2 value is defined here: http://cufflinks.cbcb.umd.edu/manual.html#gene_exp_diff 7 FPKMx 8.01089 FPKM of the gene in sample x 8 FPKMy 8.551545 FPKM of the gene in sample y 9 log2(FPKMy/FPKMx) 0.06531 The (base 2) log of the fold change y/x And log(2) in general (including a graph, which can help with visualizing) is described here (although the web is full if similar): http://en.wikipedia.org/wiki/Logarithm I can see that this same Q on seqanswers.com recieved pretty much the same answer (in brief! http://seqanswers.com/forums/showthread.php?t=19558), so I think you are safe using the data as it as generated. Taking a look at the inputs would be advised if the results were unexpected. If you do still have concerns about the log(2) calculation, asking the tool authors directly (if you have't done so already) at tophat.cufflinks@gmail.com is always an option, to tripple check. Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Jennifer Hillman Jackson
6.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hi Noa, This is it exactly - thanks for adding in the interpretation! Jen -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k
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