Question: Selecting probe data from Clariom D assays using the fid probe tags
gravatar for AliStair Rust
11 months ago by
AliStair Rust0 wrote:


I'm likely to be working with some Clariom D assays and I'm starting to do some initial explorations.

There are some example CEL files provide on the Thermo Fisher website and I'm using those as my test set.

I'm interested in being able to select specific sets of probes from the total set of probes on the assay. Having run the following code below for a single CEL file, I'm confused as to how I can use the fid of a probe to be able to select it from the associated expression set.

I can extract the probe fids using getProbeInfo but I'm stuck after that. I notice that featureData is set to "none" for the CEL data read in.

Is a probe's fid its index in the expression set matrix?




> library(oligo)
> library(affycoretools)
> d_file <- "Clariom/Clariom_D/sample_data/WTPlus_Liver_Rep1_ClariomD.CEL"
> d_data <- read.celfiles(d_file)
Platform design info loaded.
Reading in : /Clariom/Clariom_D/sample_data/WTPlus_Liver_Rep1_ClariomD.CEL


> d_data
HTAFeatureSet (storageMode: lockedEnvironment)
assayData: 6892960 features, 1 samples
  element names: exprs
  rowNames: WTPlus_Liver_Rep1_ClariomD.CEL
  varLabels: exprs dates
  varMetadata: labelDescription channel
  rowNames: WTPlus_Liver_Rep1_ClariomD.CEL
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.clariom.d.human


> d_probes <- getProbeInfo(d_data, field = c('fid', 'fsetid', 'type', 'x', 'y'))
> head(d_probes)
  fid         man_fsetid   fsetid  x y      type
1   6 PSR1700199794.hg.1 24403702  5 0 main->psr
2   8           24657315 24657315  7 0      <NA>
3   8 PSR1300152110.hg.1 24258776  7 0 main->psr
4   9 PSR0200224250.hg.1 23827198  8 0 main->psr
5  11           24587906 24587906 10 0      <NA>
6  11 PSR0300183028.hg.1 23858357 10 0 main->psr


> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=C
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] pd.clariom.d.human_3.14.1 DBI_1.0.0
 [3] RSQLite_2.1.1             affycoretools_1.50.6
 [5] oligo_1.42.0              Biostrings_2.46.0
 [7] XVector_0.18.0            IRanges_2.12.0
 [9] S4Vectors_0.16.0          Biobase_2.38.0
[11] oligoClasses_1.40.0       BiocGenerics_0.24.0



pd.clariom.d.human clariom • 180 views
ADD COMMENTlink modified 11 months ago by James W. MacDonald51k • written 11 months ago by AliStair Rust0
Answer: Selecting probe data from Clariom D assays using the fid probe tags
gravatar for James W. MacDonald
11 months ago by
United States
James W. MacDonald51k wrote:

The simple answer is yes, the fid is the row of the probe-level expression matrix.

ADD COMMENTlink written 11 months ago by James W. MacDonald51k

Thanks James.

So something like the following, for the small example above, would give me what I expect:

wish_list_probe_fids <- c(6, 8, 9, 11)

eset_filtered <- exprs(d_data)[wish_list_probe_fids]
ADD REPLYlink written 11 months ago by AliStair Rust0

If what you expect is to get rows 6,8,9 and 11, then yes.

ADD REPLYlink written 11 months ago by James W. MacDonald51k
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