Hi folks,
Using DESeq2, I've obtained log2 fold change (used to compare between two conditions), plot, heatmap ext. In addition to, I have two questions:
First, I've learnt TPM normalisation is suitable for compare gene expression level in the same sample but DESeq2 doesn't provide TPM normalisation code. How can I do TPM normalization in one sample for all interested genes from un-normalizate counts in R?
Secondly, I am wondering how can I compare one gene (for example p53) between a couple of samples(or two sample for example liver vs spleen)? Actually, heatmap gives this info but I want to graph comparing samples for one gene. Is it possible?
Could you help me, please?
Thanks
0 answers
No answers yet.
Log in to answer this question.
-
RNA-seq normalization for time-dependent analysis
written by luca.sclisizzo •
-
Can I use raw read counts from the GTEx data for cross-tissue comparison?
written by mukherjeeliana24 •
-
RNA Seq TCGA Normalization of Raw Counts Question
written by B.N. •
-
Which RUVr batch corrected output is better to calculate TPM?
written by star
-
compare gene expression between and within samples
written by zhangmeng21 •
-
Comparison of ratio of expression between two genes across samples
written by guillepalou4 •
-
CPM read count normalization: what does it mean between replicates of same group and within same re…
written by salamandra
-
What is the basis of differential expression in RNA-seq?
written by masicioglu •
-
Best-suited unit of expression to perform between-sample comparison
written by leaodel
-
Differential expression for two very different samples
written by I0110
Can you quote your source for that?
You could take the normalised counts (
counts(dds, normalized=TRUE)) and plot them as barplots (as in A: Network/Pathway Analysis from Mass Spec data ):You could also take the regularised log counts and plot these as boxplots with scatter-plot overlays (as in A: Boxplot in ggplot2 ):