Hello, I'm working with R and have obtained a table which contains 3 columns and a row for each of my genes in an RNA-seq study. The first two columns contain fold conc and log fold change, respectively, but I'm most interested in the third column and finding how many of the genes have a p.value less than 0.05. Also bonus points if you can tell me how to count genes with p-value < 0.05 and logFC > 1.
So can anyone help me write some lines in R which will count the number of genes with values less than 0.05 in the third column? Also my data is in a matrix table.
Thanks so much
(here is an illustration what I'm working with)
> head(edgeHSMvHSF$table) logConc logFC p.value tag.1 -13.67186 -0.009198564 0.9914611 tag.2 -36.72240 -26.587301949 1.0000000 tag.3 -15.82522 0.272339616 0.6033744 tag.4 -15.35435 -0.253093387 0.6161544 tag.5 -18.13806 -0.079021620 1.0000000 tag.6 -15.43403 0.868789217 0.0904064
sorry looks like those numbers won't format well here
where is the column that adjusts for multiple comparisons?
Thanks for formatting my post so the values don't look so cluttered.