[BioC] Problems selecting rows from dataframe (exprs) of GNF Atlas data....

[Sebastian Thieme]

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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor