mkatari-bioinformatics-august-2013-deseq
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Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
mkatari-bioinformatics-august-2013-deseq [2015/06/17 08:19] – mkatari | mkatari-bioinformatics-august-2013-deseq [2015/06/17 09:06] – mkatari | ||
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Then we will load the experimental design. An example is provided [[https:// | Then we will load the experimental design. An example is provided [[https:// | ||
< | < | ||
- | expdesign = read.table(pathToExpDesign) | + | expdesign = read.table(" |
</ | </ | ||
Line 85: | Line 85: | ||
#To get the genes that have FDR of 10% and save it in the output directory. | #To get the genes that have FDR of 10% and save it in the output directory. | ||
< | < | ||
- | resSig | + | resSigind |
+ | resSigrep = res[ which(res$padj < 0.1 & res$log2FoldChange < -1), ] | ||
- | outfile | + | indoutfile |
+ | repoutfile = " | ||
- | write.table(resSig, | + | write.table(resSigind, |
- | | + | |
+ | sep=" | ||
+ | col.names=T, | ||
+ | row.names=F, | ||
+ | quote=F) | ||
+ | |||
+ | write.table(resSigrep, | ||
+ | repoutfile, | ||
sep=" | sep=" | ||
col.names=T, | col.names=T, |
mkatari-bioinformatics-august-2013-deseq.txt · Last modified: 2015/08/21 14:13 by mkatari