再说一下fpkm，这个标准化方法吧，一般公司都在用，像诺禾至源这些，但是你要是用这个东西做定量也是过时了，因为这玩意没办法在样品间做比较，只能在样品内做比较，比如，你可以说在liver样品中gene1比gene2表达高，但你不能讲liver样品中的gene1比spleen样品 ...

简而言之，fpkm表示基因表达量。 你提供的图展示了你的样品里不同表达量的基因的频数分布。 比如，你的第一个样品表达量fpkm在10以上的基因有8842个。 高fpkm水平的基因表示在样本中具有较高的表达水平，可能是关键基因或者活跃的功能基因。

2013年5月16日 · I met one problem about how to choose an FPKM cut-off when using cufflinks. Could anyone provides some detailed suggestion about how to choose appropriate FPKM cut-off to judge whether the corresponding gene is expressed or not? Now my RNA-seq data(90PE, generated by Illumina Hiseq2000) had about 40 million reads per sample. Thx.

2020年8月28日 · fpkm 是通过rna-seq测转录组得到每个基因表达量水平，它是一个覆盖整个生物体的某个组织所有能表达出来的基因的表达量，你可以当成是测了整个基因组的基因表达量水平，当然也有一些基因是组织特异性或者其他原因，没有表达出来，所以测出来的fpkm 值会很 ...

2010年4月5日 · 1. New released 1.3.0, after Cuffcompare, FPKM column contains all 0, missing FPKM values even tracking files have them; 2. in all the versions of CuffDiff, if you compare different conditions against the same control samples, the FPKM in the same control samples in different comparing is different; for example,

2022年1月21日 · FPKM: FPKM的全称为Fragments Per Kilobase Million，Fragments Per Kilobase of exon model per Million mapped fragments(每千个碱基的转录每百万映射读取的fragments)。通俗讲，把比对到的某个基因的Fragment数目，除以基因的长度，其比值再除以所有基因的总长度。

2020年8月24日 · 纵坐标是FPKM的log值。有些基因的FPKM值比较大，看上去不直观，所以取对数，更方便查看。从图上看，两个处理中50%基因的log10（FPKM）都就集中在大于0.8-1.8之间（这个数只是大概，纵坐标没有给出具体数值），平均log10（FPKM）大于1小于1.5的位置。

2014年5月21日 · Therefore, I currently have a table with the FPKM values for every gene in each sample. I am trying to use the Limma R package to model and extract differentially expressed genes between these several different samples (instead of 2-by-2 comparisons that can be made using CuffDiff) and have encountered the following problem to which I would ...

2012年2月11日 · In my experience, those FPKM values can fluctuate from library to library and it's driven by a variety of factors (Iibrary size, patterns in transcript abundance, etc.). I actually was referring specifically to papers that cite the Mortazavi et al 2008 paper and use it as a means of filtering data for their own analysis.

2010年7月1日 · One way to convert FPKM values is to multiply the FPKM values with transcript length and the number of reads mapped in million. Trascript length can be obtained using HTSeq. I can't understand why it is not valid to convert FPKM values into counts and use edgeR or DESeq to test for differential expression.Especially when you want to use ...