Question: How to do the data imputation of my protein expression data(values)
gravatar for koushikayaluri
25 days 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 • 143 views
ADD COMMENTlink written 25 days ago by koushikayaluri20

There are many ways to impute, see:

ADD REPLYlink written 25 days ago by zx87548.8k

Thank you will look into it.

ADD REPLYlink written 25 days 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 25 days ago by Jean-Karim Heriche21k
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