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multiple column t test in r

hi! i am beginner student

i try to filter gene expression data

so i analysis t test each gene

but this is big problem

so many colunm...

sample type gene1 gene2 gene3 gene4...
A control  1 2  4 5
B case 2 3 4 3 1
C control 2 3 1 2
D case 2 3 1 2

how to multiple column t test and summarising ttest results?

Please help me

r rna-seq
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updated by zx8754 zx8754 • written by mmh7272 mmh7272

I guess you are looking for differential expression analysis. Please search for DEseq/edgeR tutorials and make the conditions as columns.

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written by Arup Ghosh Arup Ghosh

Thank you for your good comment !

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written by mmh7272 mmh7272

Hello mmh7272!

We believe that this post does not fit the main topic of this site.

I agree with arup. Do not start making custom statistics for gene expression analysis. There are many factors that have to be taken into account, starting from count normalization over variance estimation and FDR control. Please read the papers about tools such as DESeq2, edgeR and limma. Also use google to find blog posts and community entries towards RNA-seq and microarray data analysis. There is plenty and very good material out there. The vignettes on Bioconductor of these tools are also excellent material.

For this reason we have closed your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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