We have used an extensive re-annotation of the illuminaMousev2 probe sequences to provide additional information that is not captured in the standard Bioconductor packages. Whereas Bioconductor annotations are based on the RefSeq ID that each probe maps to, our additional mappings provide data specific to each probe on the platform. See below for details. We recommend using the probe quality as a form of filtering, and retaining only perfect or good probes for an analysis.
Details of custom mappings
illuminaMousev2listNewMappings
List all the custom re-annotation mappings provided by the package
illuminaMousev2fullReannotation
Return all the re-annotation information as a matrix
illuminaMousev2ARRAYADDRESS
Array Address code used to identify the probe at the bead-level
illuminaMousev2NUID
Lumi's nuID (universal naming scheme for oligonucleotides) Reference: Du et al. (2007), Biol Direct 2:16
illuminaMousev2PROBESEQUENCE
The 50 base sequence for the probe
illuminaMousev2PROBEQUALITY
Quality grade assigned to the probe: “Perfect” if it perfectly and uniquely matches the target transcript; “Good” if the probe, although imperfectly matching the target transcript, is still likely to provide considerably sensitive signal (up to two mismatches are allowed, based on empirical evidence that the signal intensity for 50-mer probes with less than 95% identity to the respective targets is less than 50% of the signal associated with perfect matches *); “Bad” if the probe matches repeat sequences, intergenic or intronic regions, or is unlikely to provide specific signal for any transcript; “No match” if it does not match any genomic region or transcript.
illuminaMousev2CODINGZONE
Coding status of target sequence: intergenic / intronic / Transcriptomic (“Transcriptomic” when the target transcript is non-coding or there is no information on the coding sequence)
illuminaMousev2GENOMICLOCATION
Probe's genomic coordinates (hg19 for human, mm9 for mouse or rn4 for rat)
illuminaMousev2GENOMICMATCHSIMILARITY
Percentage of similarity between the probe and its best genomic match in the alignable region, taking the probe as reference
illuminaMousev2SECONDMATCHES
Genomic coordinates of second best matches between the probe and the genome
illuminaMousev2SECONDMATCHSIMILARITY
Percentage of similarity between the probe and its second best genomic match in the alignable region, taking the probe as reference
illuminaMousev2TRANSCRIPTOMICMATCHSIMILARITY
Percentage of similarity between the probe and its target transcript in the alignable region, taking the probe as reference
illuminaMousev2OTHERGENOMICMATCHES
Genomic coordinates of sequences as alignable with the probe (in terms of number of matching nucleotides) as its main target
illuminaMousev2REPEATMASK
Overlapping RepeatMasked sequences, with number of bases overlapped by the repeat
illuminaMousev2OVERLAPPINGSNP
Overlapping annotated SNPs
illuminaMousev2ENTREZREANNOTATED
Entrez IDs
illuminaMousev2ENSEMBLREANNOTATED
Ensembl IDs
illuminaMousev2SYMBOLREANNOTATED
Gene symbol derived by re-annotation
illuminaMousev2REPORTERGROUPID
For probes marked as controls in Illuminas annotation file, these gives the type of control
illuminaMousev2REPORTERGROUPNAME
Usually a more informative name for the control type
Barbosa-Morais et al. (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Research
Examples
##See what new mappings are available
illuminaMousev2listNewMappings()
x <- illuminaMousev2PROBEQUALITY
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the PROBEQUALITY for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
##Overall table of qualities
table(unlist(xx))
x <- illuminaMousev2ARRAYADDRESS
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the ARRAYADDRESS for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
##Can do the mapping from array address to illumina ID using a revmap
y<- revmap(illuminaMousev2ARRAYADDRESS)
mapped_probes <- mappedkeys(y)
# Convert to a list
yy <- as.list(y[mapped_probes])
if(length(yy) > 0) {
# Get the ARRAYADDRESS for the first five probes
yy[1:5]
# Get the first one
yy[[1]]
}
x <- illuminaMousev2CODINGZONE
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the CODINGZONE for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
x <- illuminaMousev2PROBESEQUENCE
mapped_probes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_probes])
if(length(xx) > 0) {
# Get the PROBESEQUENCE for the first five probes
xx[1:5]
# Get the first one
xx[[1]]
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(illuminaMousev2.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: org.Mm.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaMousev2.db/illuminaMousev2NewMappings.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev2listNewMappings
> ### Title: Custom mappings added to the package
> ### Aliases: illuminaMousev2ARRAYADDRESS illuminaMousev2NUID
> ### illuminaMousev2PROBESEQUENCE illuminaMousev2PROBEQUALITY
> ### illuminaMousev2CODINGZONE illuminaMousev2GENOMICLOCATION
> ### illuminaMousev2GENOMICMATCHSIMILARITY illuminaMousev2SECONDMATCHES
> ### illuminaMousev2SECONDMATCHSIMILARITY
> ### illuminaMousev2TRANSCRIPTOMICMATCHSIMILARITY
> ### illuminaMousev2OTHERGENOMICMATCHES illuminaMousev2REPEATMASK
> ### illuminaMousev2OVERLAPPINGSNP illuminaMousev2ENTREZREANNOTATED
> ### illuminaMousev2ENSEMBLREANNOTATED illuminaMousev2SYMBOLREANNOTATED
> ### illuminaMousev2listNewMappings illuminaMousev2fullReannotation
> ### illuminaMousev2REPORTERGROUPNAME illuminaMousev2REPORTERGROUPID
> ### Keywords: datasets
>
> ### ** Examples
>
>
> ##See what new mappings are available
>
> illuminaMousev2listNewMappings()
illuminaMousev2ARRAYADDRESS()
illuminaMousev2NUID()
illuminaMousev2PROBEQUALITY()
illuminaMousev2CODINGZONE()
illuminaMousev2PROBESEQUENCE()
illuminaMousev2SECONDMATCHES()
illuminaMousev2OTHERGENOMICMATCHES()
illuminaMousev2REPEATMASK()
illuminaMousev2OVERLAPPINGSNP()
illuminaMousev2ENTREZREANNOTATED()
illuminaMousev2GENOMICLOCATION()
illuminaMousev2SYMBOLREANNOTATED()
illuminaMousev2REPORTERGROUPNAME()
illuminaMousev2REPORTERGROUPID()
illuminaMousev2ENSEMBLREANNOTATED()
>
>
> x <- illuminaMousev2PROBEQUALITY
>
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the PROBEQUALITY for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "Bad"
>
>
> ##Overall table of qualities
> table(unlist(xx))
Bad Good Good*** Good**** No match Perfect
6327 1020 74 320 1347 32537
Perfect*** Perfect****
3529 1083
>
>
>
> x <- illuminaMousev2ARRAYADDRESS
>
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the ARRAYADDRESS for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "2600193"
>
> ##Can do the mapping from array address to illumina ID using a revmap
>
> y<- revmap(illuminaMousev2ARRAYADDRESS)
>
> mapped_probes <- mappedkeys(y)
> # Convert to a list
> yy <- as.list(y[mapped_probes])
> if(length(yy) > 0) {
+ # Get the ARRAYADDRESS for the first five probes
+ yy[1:5]
+ # Get the first one
+ yy[[1]]
+ }
[1] "ILMN_1243094"
>
>
>
> x <- illuminaMousev2CODINGZONE
>
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the CODINGZONE for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "Transcriptomic?"
>
> x <- illuminaMousev2PROBESEQUENCE
>
> mapped_probes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_probes])
> if(length(xx) > 0) {
+ # Get the PROBESEQUENCE for the first five probes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "GCCCTGCCTGACCTGGAAACGTAGAGATTCTTCTGCCTCAGGTTCCAGAG"
>
>
>
>
>
>
>
> dev.off()
null device
1
>