MA plots showing average logarithmically transformed counts per million (CPM) versus the log 2 fold change for pairwise comparisons between the Transplant 2H versus Naive (top row), Transplant 24H versus Naive (middle row), and Transplant 24H versus Transplant 2H …

TPM is very similar to RPKM and FPKM. The only difference is the order of operations. Here’s how you calculate TPM: Divide the read counts by the length of each gene in kilobases. This gives you reads per kilobase (RPK). Count up all the RPK values in a sample and divide this number by 1,000,000. This is your “per million” scaling factor.

2024年1月19日 · You can plot TPM if you like. This is a measure of abundance. You can access TPM if you use tximport or tximeta to bring in the data: # this is a vector of TPM: assay(dds, "abundance")["geneX",] # you can plot this vector along with sample covariates e.g. dds$condition

2022年5月25日 · 第二种用于多个组织间的比较，Multi-tissue eQTL plot, 示意如下 所有的分析结果可以通过官网进行下载，GTEx数据库不仅仅是一个正常组织的基因表达量数据库，其eQTL分析的策略更值得我们借鉴。

2020年4月11日 · 生存分析的这个图，学名叫 Kaplan Meier plot （KM plot）。 在survival页面下，可以定义基因，癌症，OS/DFS，cutoff等。 根据cutoff，会把病人分成两群， survival plot 可以比较这两群病人的生存是否有显著差异。

2015年7月9日 · TPM is very similar to RPKM and FPKM. The only difference is the order of operations. Here’s how you calculate TPM: Divide the read counts by the length of each gene in kilobases. This gives you reads per kilobase (RPK). Count up all the RPK values in a sample and divide this number by 1,000,000. This is your “per million” scaling factor.

# Goal: use TPM values to make plots of how genes change in abundance due to dox and time

One way of doing it is first transposing the TPM count matrix (assuming you want to run PCA on the samples rather than the genes), centering it, then doing an SVD and subsequently plotting the first and second columns of the u matrix (assuming you are interested in the first and second principal components.

Interactive plot!¶ Instructions: * hover over points to see the exact TPM and count values * pan and zoom with mouse and scroll

今天就为各位介绍一下基因表达量的衡量指标：rpkm、fpkm、tpm。 RPKM：Reads Per Kilobase Million，代表每百万reads中来自于某基因每千碱基长度的reads数。 RPKM是将map到基因的read数除以map到基因组上的所有read数(以million为单位)与RNA的长度(以KB为单位)，RNA-seq中用来表示 ...