doubt about samr siggenes.table$genes.up
On 2010-05-25 10:54, Leonardo K wrote:
Hi, here's my siggenes.table$genes.up snippet. Two class unpaired SAMR analysis. "Row" "Gene ID" "Gene Name" "Score(d)" "Numerator(r)" "Denominator(s+s0)" "Fold Change" "q-value(%)" "1" "25" "RPL15P22" "RPL15P22" "-1.44115338424578" "-18" "12.4899959967968" "1.27368448239355" "0" "2" "47" "CHAF1A" "CHAF1A" "-1.44115338424578" "-18" "12.4899959967968" "1.30356683838951" "0" "3" "48" "PARP2" "PARP2" "-1.44115338424578" "-18" "12.4899959967968" "1.09780831177589" "0" "4" "52" "HMGXB4" "HMGXB4" "-1.44115338424578" "-18" "12.4899959967968" "1.22596090318945" "0" Why do I get one column more in the data block (9) than the header (8)? Looks like the second column (25,47,48,etc) does not make sense.
Presumably you are getting this from an application of write.table? If so, use the argument 'row.names = FALSE' to remove the *first* column. See the first sentence in the 'CSV files' section of ?write.table. Your second column is part of the data you're saving (probably rownames from a larger dataframe or matrix). -Peter Ehlers