HI

I use annaffy to make nice HTML tables of various forms of data, but
save "saveHTML" has changed and the wheels have fallen off. I'm not sure
is the authors intended the change in functionality or not?

In the good old days ... R2.5 with annaffy 1.8.1 if I have a data_table
(given in detail below) and use 
saveHTML(data_table,filename,title) where 
> dim(data_table)
[1] 3 4
I get the expected output 3 row and 4 columns ..example:

----cut---
<th>Accession</th>
<th>UK</th>
<th>UK_US</th>
<th>US</th>
</tr>
<tr>
<td class="character"><a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=785702">RS785702</t
d>
<td class="numeric">3.22e-253</td>
<td class="numeric">0.00463</td>
<td class="numeric">0.00617</td>
</tr>
----cut---

If I save the workspace and do saveHTML(data_table,filename,title) with
R2.7.0 annafy_1.9.6 : so using  exactly the same data_table
> dim(data_table)
[1] 3 4
I still get a 3 row 4 column table but each cell is now a list
containing all the data  in a list format (the table repeated 3 times as
a list in each cell.. 

-----cut---

<th>Accession</th>
<th>UK</th>
<th>UK_US</th>
<th>US</th>
</tr>
<tr>
<td class="list"><a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=785702">RS785702,
<a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=258415">RS258415,
<a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=7006137">RS7006137<
/td>
<td class="list">3.22e-253, 1.11e-199, 4.77e-197</td>
<td class="list">0.00463, NA, 5.18e-205</td>
<td class="list">0.00617, NA, 9.32e-119</td>
</tr>
----cut---


All the gory details are below, anyone else encountered this ? Bug or
intended ? 

Thanks
Paul








 ########################  The data table used

  > data_table
An object of class "aafTable"
Slot "probeids":
character(0)

Slot "table":
$Accession
[[1]]
[1] "<a
href=\"http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=785702\">RS785702"

[[2]]
[1] "<a
href=\"http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=258415\">RS258415"

[[3]]
[1] "<a
href=\"http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=7006137\">RS700613
7"

attr(,"class")
[1] "aafList"
attr(,"class")attr(,"package")
[1] "annaffy"

$UK
[[1]]
[1] 3.22e-253

[[2]]
[1] 1.11e-199

[[3]]
[1] 4.77e-197

attr(,"class")
[1] "aafList"
attr(,"class")attr(,"package")
[1] "annaffy"

$UK_US
[[1]]
[1] 0.00463

[[2]]
[1] NA

[[3]]
[1] 5.18e-205

attr(,"class")
[1] "aafList"
attr(,"class")attr(,"package")
[1] "annaffy"

$US
[[1]]
[1] 0.00617

[[2]]
[1] NA

[[3]]
[1] 9.32e-119

attr(,"class")
[1] "aafList"
attr(,"class")attr(,"package")
[1] "annaffy"




############################# R 2.7  annaffy output #############   :
saveHTML(data_table,filename,title) 


<html>
<head>
<title>
Top 50 in UK : with UK+US and US for comparison 
</title>
<meta http-equiv="Content-Style-Type" content="text/css">
<style type="text/css">

</style>
<script language="JavaScript">
</script>
</head>
<body bgcolor="#FFFFFF">
<h1 align="center">
Top 50 in UK : with UK+US and US for comparison 
</h1>
<table border="2">
<tr>
<th>Accession</th>
<th>UK</th>
<th>UK_US</th>
<th>US</th>
</tr>
<tr>
<td class="list"><a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=785702">RS785702,
<a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=258415">RS258415,
<a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=7006137">RS7006137<
/td>
<td class="list">3.22e-253, 1.11e-199, 4.77e-197</td>
<td class="list">0.00463, NA, 5.18e-205</td>
<td class="list">0.00617, NA, 9.32e-119</td>
</tr>
<tr>
<td class="list"><a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=785702">RS785702,
<a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=258415">RS258415,
<a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=7006137">RS7006137<
/td>
<td class="list">3.22e-253, 1.11e-199, 4.77e-197</td>
<td class="list">0.00463, NA, 5.18e-205</td>
<td class="list">0.00617, NA, 9.32e-119</td>
</tr>
<tr>
<td class="list"><a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=785702">RS785702,
<a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=258415">RS258415,
<a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=7006137">RS7006137<
/td>
<td class="list">3.22e-253, 1.11e-199, 4.77e-197</td>
<td class="list">0.00463, NA, 5.18e-205</td>
<td class="list">0.00617, NA, 9.32e-119</td>
</tr>
</table>
<p>3 Genes</p>
</body>
</html>

############

> sessionInfo()
R version 2.7.0 Under development (unstable) (2007-10-06 r43104) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
base     

other attached packages:
[1] annaffy_1.9.6   KEGG_1.99.10    GO_1.99.1       Biobase_1.15.36

loaded via a namespace (and not attached):
[1] AnnotationDbi_0.99.11 DBI_0.2-3             RSQLite_0.6-3        
> 









############################# R 2.5  annaffy output #############  :
saveHTML(data_table,filename,title)

 <html>
<head>
<title>
Top 50 in UK : with UK+US and US for comparison 
</title>
<meta http-equiv="Content-Style-Type" content="text/css">
<style type="text/css">

</style>
<script language="JavaScript">
</script>
</head>
<body bgcolor="#FFFFFF">
<h1 align="center">
Top 50 in UK : with UK+US and US for comparison 
</h1>
<table border="2">
<tr>
<th>Accession</th>
<th>UK</th>
<th>UK_US</th>
<th>US</th>
</tr>
<tr>
<td class="character"><a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=785702">RS785702</t
d>
<td class="numeric">3.22e-253</td>
<td class="numeric">0.00463</td>
<td class="numeric">0.00617</td>
</tr>
<tr>
<td class="character"><a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=258415">RS258415</t
d>
<td class="numeric">1.11e-199</td>
<td class="numeric">NA</td>
<td class="numeric">NA</td>
</tr>
<tr>
<td class="character"><a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=7006137">RS7006137<
/td>
<td class="numeric">4.77e-197</td>
<td class="numeric">5.18e-205</td>
<td class="numeric">9.32e-119</td>
</tr>
</table>
<p>3 Genes</p>
</body>
</html>


> sessionInfo()
R version 2.5.0 (2007-04-23) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"
"datasets"  "methods"   "base"     

other attached packages:
 annaffy     KEGG       GO  Biobase 
 "1.8.1" "1.16.0" "1.16.0" "1.14.0"
>

	[[alternative HTML version deleted]]

