doubt about samr siggenes.table$genes.up
Leo, This question is more suited for the BioC help list. Please post your question over there. Also, offer more info about how you arrived this siggenes.table, what version of R and siggenes package you're using would be helpful. Please read the posting guide! ...Tao ----- Original Message ----
From: Peter Ehlers <ehlers at ucalgary.ca> To: Leonardo K <shikida at gmail.com> Cc: r-help at r-project.org Sent: Tue, May 25, 2010 1:41:36 PM Subject: Re: [R] doubt about samr siggenes.table$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
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PLEASE do read the posting
and provide commented,
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