Question: Calculating a score from fold change matrix of pair-wise rna-seq data
gravatar for g.atla
3.7 years ago by
g.atla0 wrote:

I have RNA-Seq data with paired design, each tissue with treatment and untreated data. I have used DESeq2, using normTransform(), to calculate the pairwise fold-changes. So Initially I have 60 samples  and now I have a Fold change matrix of 30 columns and for all genes.

GeneID    sample1_T    sample1_U    sample2_T    sample2_U    .    .    .    sample30_U
gene1    n    n    n    n    .    .    .    
gene2     n    n    n   n    .    .   .

FC Matrix:

GeneID    sample1    sample2    .    .    .   .    sample30
gene1    -3.11    -1.3    .    .    .    .    -0.5
gene2    3.12    1.12    .    .    .    .    0.5

Now I would like to filter the data such that the genes which are consistently up/down-regulated in at least 80% of the samples or 60% of the samples, genes that does not have any consistent up/down regulation etc. 

I would like to calculate a statistical score which represents the number of samples the gene shown to be up/down regulated and extent of fold change, such that I can use that score to filter the matrix.

I did a DE analysis using the paired-design and tried to use the adj-Pvalue for filtering the data, but I do not know (Edit) if I can use this to filter as per my criterial. 

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by g.atla0

I'll just leave a comment instead of answer, and leave it open for anyone else to answer. I read your post but I don't have any concrete suggestions for you. If you want to derive a new statistic and then estimate its distributional properties, you might want to consider collaborating with a statistician.

ADD REPLYlink written 3.7 years ago by Michael Love26k

I am trying to do this because, in my data, DE of some genes is supported by only few samples, which have high regulation, so I am trying to filter the data such that the DE is supported 90% of samples or 80% of samples etc. So I am checking if there is any way to calculate a score.  

For example, the heat map of Fold-change shows that there are genes ( marked in white box) that have high FC values in subset of samples. 

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by g.atla0

Note that the standard significance test is of the null hypothesis (no differences) which will eventually be rejected even if a subset of the pairs show differences.

This is similar to a t-test, where you compare say rnorm(2*n,0) with c(rnorm(n,0),rnorm(n,1)). The second group is bimodal, and so the model is not well specified, but the t-test will eventually reject the null even though half the samples in the second group are iid as the first group. Null hypothesis testing can only get you so far.

It sounds to me like this might be a case for clustering or other unsupervised machine learning techniques. The null hypothesis test p-value only gives a limited amount of information here, where the data can be mined in a more rich way.

ADD REPLYlink written 3.7 years ago by Michael Love26k
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