[BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....
Bas Jansen
bjhjansen at gmail.com
Tue Jan 3 15:37:28 CET 2012
Hi Axel, hi Sebastian:
Thanks for the cookie, Axel. Anyway, I have done the following:
> exprs <- as.dataframe(exprs(eset))
> rownames(exprs)
[1] "200000_s_at" "200001_at"
[3] "200002_at" "200003_s_at"
[5] "200004_at" "200005_at"
[7] "200006_at" "200007_at"
[9] "200008_s_at" "200009_at"
[11] "200010_at" "200011_s_at"
[13] "200012_x_at" "200013_at"
[15] "200014_s_at" "200015_s_at"
[17] "200016_x_at" "200017_at"
etc.
So I would argue that the 'numbers' are recognized as rownames here,
but I cannot select them as indicated in a previous email. Strange,
isn't it?
I still need to try Sebastian's suggestions though, so let's not run
off the cliff just yet. Below the sessionInfo.
Kind regards,
Bas
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] C/UTF-8/C/C/C/C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] fortunes_1.4-2 Biobase_2.14.0
loaded via a namespace (and not attached):
[1] tcltk_2.14.0 tools_2.14.0
On Tue, Jan 3, 2012 at 2:33 PM, <axel.klenk at actelion.com> wrote:
> Dear Bas,
>
> I think you'll need to show us your original code, in particular what your
> 'exprs' is
> and how you have obtained it. If you have "extracted the expression
> values" from
> an ExpressionSet ES like
>
> x <- exprs(ES)
>
> then x is a matrix and not a data.frame -- but then your output would look
> slightly
> different. If you have done something like
>
> x <- data.frame(exprs(ES))
>
> I can reproduce your output, including rows that are all NA -- for
> rownames that
> do not exist.
>
> So: how did you create 'exprs' and are you sure your rownames are ok?
>
> Cheers,
>
> - axel
>
>
> BTW: try
>
> install.packages("fortunes")
> library("fortunes")
> fortune("dog")
>
> to see why 'exprs' may not be a good name for your object... :-)
>
>
>
> Axel Klenk
> Research Informatician
> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
> Switzerland
>
>
>
>
> From:
> Bas Jansen <bjhjansen at gmail.com>
> To:
> Sebastian Thieme <thieme at mi.fu-berlin.de>
> Cc:
> bioconductor at r-project.org
> Date:
> 03.01.2012 13:48
> Subject:
> Re: [BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas
> data....
> Sent by:
> bioconductor-bounces at r-project.org
>
>
>
> Dear Sebastian:
>
> Thanks for your swift reply. It works, but only for the probe ID that
> start with a character (only ~15 out of the > 100 probe IDs I want to
> investigate). Those that start with a number report back with "<0
> rows> (or 0-length row.names)". The motto for the New Year seems to be
> 'Solve a problem, only to find new ones'. Phew.
>
> Kind regards,
> Bas
>
> On Tue, Jan 3, 2012 at 11:19 AM, Sebastian Thieme
> <thieme at mi.fu-berlin.de> wrote:
>> Hello,
>>
>> happy new year too =)
>>
>> you can use exprs[ rownames(exprs) %in% "gnf1h00499_at",] or exprs[
>> rownames(exprs) %in% vectorOfNames,], where vectorOfNames is a list or
>> a vector of the names you are looking for. Important is that the
>> object you are search in has to be the first argument. If you want
>> requesting a high number of names use lists instead of dataframes.
>>
>> best
>>
>> Basti
>>
>> 2012/1/3 Bas Jansen <bjhjansen at gmail.com>:
>>> Dear fellow Bioconductor users:
>>>
>>> Happy New Year!
>>> At the moment I am analyzing the GNF Atlas data. I retrieved the data
>>> from the Gene Expression Omnibus using the package GEOquery, converted
>>> it to an expressionSet and extracted the expression values. So now I
>>> have a data frame from which I would like to extract the expression
>>> values of > 100 probe IDs for 79 tissues. Thing is, if I use a single
>>> probe ID, things go fine. However, whenever I use a string of probe
>>> IDs, things go awry.
>>>
>>> See below:
>>>
>>> ***
>>>> exprs[c("gnf1h00499_at"),]
>>> GSM18768 GSM18769 GSM18756 GSM18757 GSM18780 GSM18781
> GSM18774
>>> gnf1h00499_at 5.770829 7.708739 5.161888 7.459432 6.332708 6.902074
> 4.472488
>>> (abbreviated for reasons of clarity)
>>> ***
>>>
>>> As stated above: whenever I use a string of probe IDs (say, like 2
>>> probe IDs), things go awry:
>>>
>>> ***
>>>> exprs[c("gnf1h00499_at","gnf1h500_at"),]
>>> GSM18768 GSM18769 GSM18756 GSM18757 GSM18780 GSM18781
> GSM18774
>>> gnf1h00499_at 5.770829 7.708739 5.161888 7.459432 6.332708 6.902074
> 4.472488
>>> NA NA NA NA NA NA NA
> NA
>>> etc.
>>> ***
>>>
>>> The gnf1h00500 probe is reported as NA, and I'm pretty sure it has
>>> real expression values associated with it.
>>> The following just works fine:
>>>
>>> ***
>>>> exprs[c(1:20,30:70),]
>>> GSM18768 GSM18769 GSM18756 GSM18757 GSM18780 GSM18781
> GSM18774
>>> 200000_s_at 0 0 0 0 0 0
> 0
>>> 200001_at 0 0 0 0 0 0
> 0
>>> 200002_at 0 0 0 0 0 0
> 0
>>> 200003_s_at 0 0 0 0 0 0
> 0
>>> etc.
>>> ***
>>>
>>> So, how do I select rows on the basis of probe IDs? Or better yet:
>>> what am I overlooking????
>>>
>>> Thanks & kind regards,
>>> Bas
>>>
>>> _______________________________________________
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