On Fri, Feb 26, 2010 at 6:40 PM, Benilton Carvalho
<beniltoncarvalho at="" gmail.com=""> wrote:
> If you're using the latest oligo, you can use the (not exposed -
still
> working on further details) function getFidProbeset() :
>
> probeInfo = oligo:::getFidProbeset(rawdata)
> idx = probeInfo[["fid"]]
> ## probeset names are in probeInfo[["fsetid"]]
> intensities = exprs(rawdata)[idx,]
> and work with 'intensities' (which includes the PMs and controls).
Thank you! It works!
> If you rather use only PMs:
>
> pms = pm(rawdata)
> pns = probeNames(rawdata)
> these are now regular matrices and you can use
> rma.background.correct() and normalize.quantiles().
Here I have got a problem. probeNames() does not work with my dataset.
pms = pm(rawdata)
pns = probeNames(rawdata)
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: no such column: man_fsetid)
Best regards,
Mikhail
my bad... that's a mod that never made it to the code... in the
meantime, can you please run the following bit once (which will set
probeNames and after which everything will be fine):
setMethod("probeNames", "GeneFeatureSet",
function(object, subset=NULL){
res <- dbGetQuery(db(object), "SELECT fsetid FROM
pmfeature")[[1]]
as.character(res)
})
b
On Mon, Mar 1, 2010 at 10:53 AM, Mikhail Pachkov <pachkov at="" gmail.com=""> wrote:
> On Mon, Mar 1, 2010 at 11:51 AM, Benilton Carvalho
> <beniltoncarvalho at="" gmail.com=""> wrote:
>> can you give me the results for sessionInfo()?
>
> ?sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-unknown-linux-gnu
>
> locale:
> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C
> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8
> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8
> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C
> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
>
> other attached packages:
> [1] pd.hugene.1.0.st.v1_3.0.0 RSQLite_0.8-3
> [3] DBI_0.2-5 ? ? ? ? ? ? ? ? oligo_1.10.2
> [5] preprocessCore_1.8.0 ? ? ?oligoClasses_1.8.0
> [7] Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.18.0 ?affyio_1.14.0 ? ? ?Biostrings_2.14.12
IRanges_1.4.11
> [5] splines_2.10.1 ? ? tools_2.10.1
>
On Mon, Mar 1, 2010 at 12:06 PM, Benilton Carvalho
<beniltoncarvalho at="" gmail.com=""> wrote:
> my bad... that's a mod that never made it to the code... in the
> meantime, can you please run the following bit once (which will set
> probeNames and after which everything will be fine):
>
> setMethod("probeNames", "GeneFeatureSet",
> ? ? ? ? ? ? ? ? ?function(object, subset=NULL){
> ? ? ? ? ? ? ? ? ? ?res <- dbGetQuery(db(object), "SELECT fsetid FROM
> pmfeature")[[1]]
> ? ? ? ? ? ? ? ? ? ?as.character(res)
> ? ? ? ? ? ? ? ? ?})
That works. Thank you! However I need both fsetid and fid so I tried
to modify the method a little:
setMethod("probeNames", "GeneFeatureSet",
function(object, subset=NULL){
res <- dbGetQuery(db(object), "SELECT fid,fsetid
FROM
pmfeature")
paste(res[,1],res[,2])
})
Could you tell me if that is correct way to get fid, fsetid pairs for
pms?
Thank you in advance.
Best regards,
Mikhail
don't change the probeNames method.
Use probeNames() to get the (character version) of fsetid and
pmindex() to get the fid.
b
On Mon, Mar 1, 2010 at 4:50 PM, Mikhail Pachkov <pachkov at="" gmail.com="">
wrote:
> On Mon, Mar 1, 2010 at 12:06 PM, Benilton Carvalho
> <beniltoncarvalho at="" gmail.com=""> wrote:
>> my bad... that's a mod that never made it to the code... in the
>> meantime, can you please run the following bit once (which will set
>> probeNames and after which everything will be fine):
>>
>> setMethod("probeNames", "GeneFeatureSet",
>> ? ? ? ? ? ? ? ? ?function(object, subset=NULL){
>> ? ? ? ? ? ? ? ? ? ?res <- dbGetQuery(db(object), "SELECT fsetid
FROM
>> pmfeature")[[1]]
>> ? ? ? ? ? ? ? ? ? ?as.character(res)
>> ? ? ? ? ? ? ? ? ?})
>
> That works. Thank you! However I need both fsetid and fid so I tried
> to modify the method a little:
>
> setMethod("probeNames", "GeneFeatureSet",
> ? ? ? ? ? ? ? ? function(object, subset=NULL){
> ? ? ? ? ? ? ? ? ? res <- dbGetQuery(db(object), "SELECT fid,fsetid
FROM
> pmfeature")
> ? ? ? ? ? ? ? ? ? paste(res[,1],res[,2])
> ? ? ? ? ? ? ? ? })
>
> Could you tell me if that is correct way to get fid, fsetid pairs
for pms?
>
> Thank you in advance.
>
> Best regards,
>
> Mikhail
>
Dear Benilton,
I have got a problem obtaining probe indices along with probe names.
My script:
library(oligo);
workingDir = getwd();
celfiles<-list.files(path=workingDir,pattern=".CEL$|.cel$");
rawdata=read.celfiles(celfiles);
pms = pm(rawdata)
rmadata=rma.background.correct(pms)
qndata=normalize.quantiles(log2(rmadata))
res <- dbGetQuery(db(rawdata), "SELECT fsetid,atom,fid FROM
pmfeature")
pid=paste(res[,1],res[,2],res[,3],sep=":")
rownames(qndata)<-pid
colnames(qndata)<-sampleNames(rawdata)
However during analysis of the data it looked like probe names were
determined wrong. I have tried to use pmindex() to extract "fid" of pm
probes which seems to be a list of numbers sorted in ascending order.
I do the following:
pnames=probeNames(rawdata)
length(pnames)
[1] 818005
pmidx=pmindex(rawdata)
length(pmidx)
[1] 818005
# first value in probe names
pnames[1]
[1] "7896737"
# first value in pm indices
pmidx[1]
[1] 1056
If I check pgf file for probe with index "1056", it belongs to
probeset "7981328" not "7896737" as it given in pnames.
My question: How to obtain probeset-probe_id pairs in correct order
for annotating expression values in "pms" matrix?
Best regards,
Mikhail
what's the array you're looking at?
sessionInfo()?
thanks,
b
On Mon, Mar 22, 2010 at 10:54 AM, Mikhail Pachkov <pachkov at="" gmail.com=""> wrote:
> Dear Benilton,
>
> I have got a problem obtaining probe indices along with probe names.
My script:
>
> library(oligo);
> workingDir = getwd();
> celfiles<-list.files(path=workingDir,pattern=".CEL$|.cel$");
> rawdata=read.celfiles(celfiles);
>
> pms = pm(rawdata)
> rmadata=rma.background.correct(pms)
> qndata=normalize.quantiles(log2(rmadata))
>
> res <- dbGetQuery(db(rawdata), "SELECT fsetid,atom,fid FROM
pmfeature")
> pid=paste(res[,1],res[,2],res[,3],sep=":")
> rownames(qndata)<-pid
>
> colnames(qndata)<-sampleNames(rawdata)
>
> However during analysis of the data it looked like probe names were
> determined wrong. I have tried to use pmindex() to extract "fid" of
pm
> probes which seems to be a list of numbers sorted in ascending
order.
> I do the following:
>
> pnames=probeNames(rawdata)
> length(pnames)
> [1] 818005
>
> pmidx=pmindex(rawdata)
> length(pmidx)
> [1] 818005
>
> # first value in probe names
> pnames[1]
> [1] "7896737"
>
> # first value in pm indices
> pmidx[1]
> [1] 1056
>
> If I check pgf file for probe with index "1056", it belongs to
> probeset "7981328" not "7896737" as it given in pnames.
>
> My question: How to obtain probeset-probe_id pairs in correct order
> for annotating expression values in "pms" matrix?
>
> Best regards,
>
> Mikhail
>
Dear Mikhail,
I was able to reproduce the issue you reported. The probeNames()
method in 1.10.3 is missing a sort by fid.
setMethod("probeNames", "GeneFeatureSet",
function(object, subset=NULL){
res <- dbGetQuery(db(object), "SELECT fsetid FROM
pmfeature ORDER BY fid")[[1]]
as.character(res)
})
I'll get this fixed now.
b
On Mon, Mar 22, 2010 at 11:04 AM, Benilton Carvalho
<beniltoncarvalho at="" gmail.com=""> wrote:
> what's the array you're looking at?
>
> sessionInfo()?
>
> thanks,
> b
>
> On Mon, Mar 22, 2010 at 10:54 AM, Mikhail Pachkov <pachkov at="" gmail.com=""> wrote:
>> Dear Benilton,
>>
>> I have got a problem obtaining probe indices along with probe
names. My script:
>>
>> library(oligo);
>> workingDir = getwd();
>> celfiles<-list.files(path=workingDir,pattern=".CEL$|.cel$");
>> rawdata=read.celfiles(celfiles);
>>
>> pms = pm(rawdata)
>> rmadata=rma.background.correct(pms)
>> qndata=normalize.quantiles(log2(rmadata))
>>
>> res <- dbGetQuery(db(rawdata), "SELECT fsetid,atom,fid FROM
pmfeature")
>> pid=paste(res[,1],res[,2],res[,3],sep=":")
>> rownames(qndata)<-pid
>>
>> colnames(qndata)<-sampleNames(rawdata)
>>
>> However during analysis of the data it looked like probe names were
>> determined wrong. I have tried to use pmindex() to extract "fid" of
pm
>> probes which seems to be a list of numbers sorted in ascending
order.
>> I do the following:
>>
>> pnames=probeNames(rawdata)
>> length(pnames)
>> [1] 818005
>>
>> pmidx=pmindex(rawdata)
>> length(pmidx)
>> [1] 818005
>>
>> # first value in probe names
>> pnames[1]
>> [1] "7896737"
>>
>> # first value in pm indices
>> pmidx[1]
>> [1] 1056
>>
>> If I check pgf file for probe with index "1056", it belongs to
>> probeset "7981328" not "7896737" as it given in pnames.
>>
>> My question: How to obtain probeset-probe_id pairs in correct order
>> for annotating expression values in "pms" matrix?
>>
>> Best regards,
>>
>> Mikhail
>>
>
btw, the following is faster:
setMethod("probeNames", "GeneFeatureSet",
function(object, subset=NULL){
res <- dbGetQuery(db(object), "SELECT fid, fsetid
FROM pmfeature ORDER BY fid")
idx <- order(res[["fid"]])
as.character(res[idx, "fsetid"])
})
b
On Mon, Mar 22, 2010 at 11:18 AM, Benilton Carvalho
<beniltoncarvalho at="" gmail.com=""> wrote:
> Dear Mikhail,
>
> I was able to reproduce the issue you reported. The ?probeNames()
> method in 1.10.3 is missing a sort by fid.
>
> setMethod("probeNames", "GeneFeatureSet",
> ? ? ? ? ? ? ? ? function(object, subset=NULL){
> ? ? ? ? ? ? ? ? ? res <- dbGetQuery(db(object), "SELECT fsetid FROM
> pmfeature ORDER BY fid")[[1]]
> ? ? ? ? ? ? ? ? ? as.character(res)
> ? ? ? ? ? ? ? ? })
>
> I'll get this fixed now.
>
> b
>
> On Mon, Mar 22, 2010 at 11:04 AM, Benilton Carvalho
> <beniltoncarvalho at="" gmail.com=""> wrote:
>> what's the array you're looking at?
>>
>> sessionInfo()?
>>
>> thanks,
>> b
>>
>> On Mon, Mar 22, 2010 at 10:54 AM, Mikhail Pachkov <pachkov at="" gmail.com=""> wrote:
>>> Dear Benilton,
>>>
>>> I have got a problem obtaining probe indices along with probe
names. My script:
>>>
>>> library(oligo);
>>> workingDir = getwd();
>>> celfiles<-list.files(path=workingDir,pattern=".CEL$|.cel$");
>>> rawdata=read.celfiles(celfiles);
>>>
>>> pms = pm(rawdata)
>>> rmadata=rma.background.correct(pms)
>>> qndata=normalize.quantiles(log2(rmadata))
>>>
>>> res <- dbGetQuery(db(rawdata), "SELECT fsetid,atom,fid FROM
pmfeature")
>>> pid=paste(res[,1],res[,2],res[,3],sep=":")
>>> rownames(qndata)<-pid
>>>
>>> colnames(qndata)<-sampleNames(rawdata)
>>>
>>> However during analysis of the data it looked like probe names
were
>>> determined wrong. I have tried to use pmindex() to extract "fid"
of pm
>>> probes which seems to be a list of numbers sorted in ascending
order.
>>> I do the following:
>>>
>>> pnames=probeNames(rawdata)
>>> length(pnames)
>>> [1] 818005
>>>
>>> pmidx=pmindex(rawdata)
>>> length(pmidx)
>>> [1] 818005
>>>
>>> # first value in probe names
>>> pnames[1]
>>> [1] "7896737"
>>>
>>> # first value in pm indices
>>> pmidx[1]
>>> [1] 1056
>>>
>>> If I check pgf file for probe with index "1056", it belongs to
>>> probeset "7981328" not "7896737" as it given in pnames.
>>>
>>> My question: How to obtain probeset-probe_id pairs in correct
order
>>> for annotating expression values in "pms" matrix?
>>>
>>> Best regards,
>>>
>>> Mikhail
>>>
>>
>
My copy/paste skills need to be improved. Apologies.
setMethod("probeNames", "GeneFeatureSet",
function(object, subset=NULL){
res <- dbGetQuery(db(object), "SELECT fid, fsetid FROM
pmfeature")
idx <- order(res[["fid"]])
as.character(res[idx, "fsetid"])
})
On Mon, Mar 22, 2010 at 11:20 AM, Benilton Carvalho
<beniltoncarvalho at="" gmail.com=""> wrote:
> btw, the following is faster:
>
> setMethod("probeNames", "GeneFeatureSet",
> ? ? ? ? ? ? ? ? function(object, subset=NULL){
> ? ? ? ? ? ? ? ? ? res <- dbGetQuery(db(object), "SELECT fid, fsetid
> FROM pmfeature ORDER BY fid")
> ? ? ? ? ? ? ? ? ? idx <- order(res[["fid"]])
> ? ? ? ? ? ? ? ? ? as.character(res[idx, "fsetid"])
> ? ? ? ? ? ? ? ? })
>
> b
>
> On Mon, Mar 22, 2010 at 11:18 AM, Benilton Carvalho
> <beniltoncarvalho at="" gmail.com=""> wrote:
>> Dear Mikhail,
>>
>> I was able to reproduce the issue you reported. The ?probeNames()
>> method in 1.10.3 is missing a sort by fid.
>>
>> setMethod("probeNames", "GeneFeatureSet",
>> ? ? ? ? ? ? ? ? function(object, subset=NULL){
>> ? ? ? ? ? ? ? ? ? res <- dbGetQuery(db(object), "SELECT fsetid FROM
>> pmfeature ORDER BY fid")[[1]]
>> ? ? ? ? ? ? ? ? ? as.character(res)
>> ? ? ? ? ? ? ? ? })
>>
>> I'll get this fixed now.
>>
>> b
>>
>> On Mon, Mar 22, 2010 at 11:04 AM, Benilton Carvalho
>> <beniltoncarvalho at="" gmail.com=""> wrote:
>>> what's the array you're looking at?
>>>
>>> sessionInfo()?
>>>
>>> thanks,
>>> b
>>>
>>> On Mon, Mar 22, 2010 at 10:54 AM, Mikhail Pachkov <pachkov at="" gmail.com=""> wrote:
>>>> Dear Benilton,
>>>>
>>>> I have got a problem obtaining probe indices along with probe
names. My script:
>>>>
>>>> library(oligo);
>>>> workingDir = getwd();
>>>> celfiles<-list.files(path=workingDir,pattern=".CEL$|.cel$");
>>>> rawdata=read.celfiles(celfiles);
>>>>
>>>> pms = pm(rawdata)
>>>> rmadata=rma.background.correct(pms)
>>>> qndata=normalize.quantiles(log2(rmadata))
>>>>
>>>> res <- dbGetQuery(db(rawdata), "SELECT fsetid,atom,fid FROM
pmfeature")
>>>> pid=paste(res[,1],res[,2],res[,3],sep=":")
>>>> rownames(qndata)<-pid
>>>>
>>>> colnames(qndata)<-sampleNames(rawdata)
>>>>
>>>> However during analysis of the data it looked like probe names
were
>>>> determined wrong. I have tried to use pmindex() to extract "fid"
of pm
>>>> probes which seems to be a list of numbers sorted in ascending
order.
>>>> I do the following:
>>>>
>>>> pnames=probeNames(rawdata)
>>>> length(pnames)
>>>> [1] 818005
>>>>
>>>> pmidx=pmindex(rawdata)
>>>> length(pmidx)
>>>> [1] 818005
>>>>
>>>> # first value in probe names
>>>> pnames[1]
>>>> [1] "7896737"
>>>>
>>>> # first value in pm indices
>>>> pmidx[1]
>>>> [1] 1056
>>>>
>>>> If I check pgf file for probe with index "1056", it belongs to
>>>> probeset "7981328" not "7896737" as it given in pnames.
>>>>
>>>> My question: How to obtain probeset-probe_id pairs in correct
order
>>>> for annotating expression values in "pms" matrix?
>>>>
>>>> Best regards,
>>>>
>>>> Mikhail
>>>>
>>>
>>
>
