[R] doubt about samr siggenes.table$genes.up

[Shi, Tao]

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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