Question: How to do the data imputation of my protein expression data(values)
gravatar for koushikayaluri
4 months ago by
koushikayaluri20 wrote:

I am currently working on a protein expression data of breast cancer where rows are my proteins (Refseq) and columns are my samples. I have 77 cancer affected samples, 3 replicates and 3 normal samples and have a lot of missing values. My data is normalized and contains log2 iTRAQ ratios of each sample. I want to do data imputation of my data and working in R and confused about what data package should I use for the data imputation or what should be my approach towards the data as I am planning to perform gene set analysis using the GSA package in R. And can I do a PCA plot to find out how the cancer subtypes are distributed across the sample?

Thanks in advance.


alignment rna-seq next-gen R gene • 195 views
ADD COMMENTlink written 4 months ago by koushikayaluri20

There are many ways to impute, see:

ADD REPLYlink written 4 months ago by zx87549.1k

Thank you will look into it.

ADD REPLYlink written 4 months ago by koushikayaluri20

Do you need imputation to start with? For example, there are ways of doing PCA with missing values (e.g. this paper).

ADD REPLYlink written 4 months ago by Jean-Karim Heriche22k
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