[BioC] How to write "matchprobes" result(list of vector) to a table?

[lgautier@altern.org]

> Dr. Gautier,
> I found there were two versions of alternative mappings in your original
> paper. I want to know which version the "matchprobes" create the
> alternative
> mapping for. I guess the output contains all possible matches.
> My plan was to write the "matchprobes" output object into a database, in
> which each row is a match. And use MS Excel or Access to figure out the
> logic of the function "matchpobes", then eliminate some probes if
> necessory.
> And I did figure out a way to do that. Here is the code: (m is the
> "matchprobes" output object)
> sink("probe match table.txt")
> for(i in 1: length(m[[1]])) {
> 	if (length(m[[1]][[i]])==0) {
> 		print(c(i, 0))
> 	}
> 	else {
> 		for ( j in 1: length(m[[1]][[i]])){
> 			print ( c(i, m[[1]][[i]][[j]], m[[2]][[i]][[j]]))
> 		}
> 	}
> }
> sink()
> Until now, I don't have chance to import the text file into database table
> yet.
> If you can show me how you got the two versions of alternative and explain
> the "matchprobes" function in detail, that will be great.

The data files you refer to were obtained exactly as described in the
vignette.
If the documentation is not sufficient, following step by step what a
function is doing is achieved easily with the command 'debug'.
Note that in the case of 'matchprobes' C code is called, and this will
look like a black box until you read the source for it.


Hoping this helps,


L.


> By the way, I did save the object "three times" as soon as probe matching
> done.
> Thanks.
>
> Lingsheng
>
>
>
>
>
>
> The fear of the LORD is the beginning of wisdom, and knowledge of the Holy
> One is understanding.
> --Proverbs 10:10
>
>
>
>
>
>>From: lgautier at altern.org
>>To: "Lingsheng Dong" <dong_lsh at hotmail.com>
>>CC: bioconductor at stat.math.ethz.ch
>>Subject: Re: [BioC] How to write "matchprobes" result(list of vector) to
>> a
>>     table?
>>Date: Mon, 7 Nov 2005 15:36:18 +0100 (CET)
>>
>> > Hi, all,
>> > I want to use most updated RefSeq to map Affymetrix probes and
>> eliminate
>> > cross hybredization probes as Dr. Gautier did
>> > http://www.biomedcentral.com/1471-2105/5/111.
>> >
>> > Now the probe matching is finialy finished after the funtion
>>"matchprobes"
>> > run for 150 hours.
>>
>>Not completely unexpected. At the time, I remember parallelizing the job
>>to make use of several processors...
>>
>> > I want export the matchprobes result to a table. I
>> > checked the documentation, saying the result is list of vector.
>> > Is there a specicial funtion to do it or I need to loop through the
>> list
>> > and
>> > write the content to a text file?
>>
>>This is most likely the way to go.
>>If you want everything in one table, you may have the need for
>> refinements
>>since the output list (or the two lists if 'probepos=TRUE') has one
>>element per reference sequence in the input, but can have 0 to many
>>matches for
>>each one of these elements.
>>
>>If you are unsure, first save your list (R command 'save'), as it
>>represents 150 hours of (computer) work.
>>
>>
>>Hoping this helps,
>>
>>
>>
>>Laurent
>>
>>
>>
>> > Thanks a lot.
>> >
>> > Lingsheng
>> >
>> >
>> >
>> >
>> >
>> >
>> > The fear of the LORD is the beginning of wisdom, and knowledge of the
>>Holy
>> > One is understanding.
>> > --Proverbs 10:10
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >
>>
>>
>
>
>