To whom it may concern,
I am following this tutorial: https://www2.unil.ch/cbg/homepage/downloads/tissues.pdf to process sample from GSE14578_RAW.tar: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14578
The code is as below:
Anyone know how to address the error in the end?
Thanks in advance.
Jianhai
It is working! But, please note:
According to James: "... so I have added code to both the release and devel version of AnnotationDbi to do this for the arabidopsis chips as well."
The current release version of BioC is version 3.5, to be used with R version 3.4.0. See here.
You are using R version 3.3.0 (2016-05-03), which uses BioC version 3.4. In other words, you are lagging behind and will have to update R and BioC to make use of the 'fixed' functionality.
> library(ath1121501.db) > head(toTable(ath1121501ENTREZID)) probe_id gene_id 1 261585_at 839580 2 261568_at 839321 3 261584_at 839574 4 261579_at 839579 5 261569_at 839341 6 261576_at 839550 > sessionInfo() R version 3.4.0 Patched (2017-05-10 r72670) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] ath1121501.db_3.2.3 org.At.tair.db_3.4.1 AnnotationDbi_1.38.1 [4] IRanges_2.10.2 S4Vectors_0.14.2 Biobase_2.36.2 [7] BiocGenerics_0.22.0 BiocInstaller_1.26.0 loaded via a namespace (and not attached): [1] compiler_3.4.0 DBI_0.6-1 tools_3.4.0 memoise_1.1.0 Rcpp_0.12.11 [6] RSQLite_1.1-2 digest_0.6.12 >
There is no ath1121501ENTREZID Bimap object, which is why you get that error. There is an ENTREZID column for the org.At.tair package, so hypothetically there could (or should) be one, but the central ID for Arabidopsis is the TAIR ID, so maybe that's why it doesn't exist.
Hypothetically we could go back and add one in, but the better course of action would be for Gabor Csardi to update his package to take advantage of the more modern select interface rather than relying on Bimaps, which are only there for backward compatibility.
The Bimaps are created by the AnnotationDbi package when you load the ath1121501.db package. This is technically a bug (the ENTREZID Bimap exists for the org.At.tair.db package, but not for the chip packages), so I have added code to both the release and devel version of AnnotationDbi to do this for the arabidopsis chips as well.
> library(ath1121501.db) <snip> > ls(2) [1] "ath1121501" "ath1121501ACCNUM" "ath1121501ARACYC" [4] "ath1121501ARACYCENZYME" "ath1121501CHR" "ath1121501CHRLENGTHS" [7] "ath1121501CHRLOC" "ath1121501CHRLOCEND" "ath1121501.db" [10] "ath1121501_dbconn" "ath1121501_dbfile" "ath1121501_dbInfo" [13] "ath1121501_dbschema" "ath1121501ENTREZID" "ath1121501ENZYME" [16] "ath1121501ENZYME2PROBE" "ath1121501GENENAME" "ath1121501GO" [19] "ath1121501GO2ALLPROBES" "ath1121501GO2PROBE" "ath1121501MAPCOUNTS" [22] "ath1121501ORGANISM" "ath1121501ORGPKG" "ath1121501PATH" [25] "ath1121501PATH2PROBE" "ath1121501PMID" "ath1121501PMID2PROBE" [28] "ath1121501SYMBOL" > head(toTable(ath1121501ENTREZID)) probe_id gene_id 1 261585_at 839580 2 261568_at 839321 3 261584_at 839574 4 261579_at 839579 5 261569_at 839341 6 261576_at 839550
The updated version will propagate through the build servers in a day or so, and you can get with biocLite.
Hello James,
Thanks for adding the Entres Bimap.
But when I followed the instructions (https://bioconductor.org/packages/release/data/annotation/html/ath1121501.db.html) to install ath1121501.db, and library(), then ls(2). There is still no "ath1121501ENTREZID".
Is it not available yet?
The sessionInfor:
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
locale:
[1] C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] ath1121501.db_3.2.3 org.At.tair.db_3.4.0 AnnotationDbi_1.36.2
[4] IRanges_2.8.1 S4Vectors_0.12.1 Biobase_2.34.0
[7] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] DBI_0.5-1 memoise_1.1.0 Rcpp_0.12.11 RSQLite_1.1-2 digest_0.6.12
Regards,
Jianai
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version 2.3.6
library(affy); library(limma); library(ape); library(gplots); library(Category);
library(ath1121501.db); library(GOstats); library(ath1121501cdf); library(eisa); library(gcrma); library(GO.db); library(KEGG.db); library(xtable)
(Extraction of control samples ommited)
#Control samples
con.mo
[1] "GSM361976.cel" "GSM361977.cel" "GSM361980.cel" "GSM361981.cel"
[5] "GSM361984.cel" "GSM361985.cel" "GSM361988.cel" "GSM361989.cel"
[9] "GSM361992.cel" "GSM361993.cel" "GSM362168.CEL" "GSM362169.CEL"
[13] "GSM362170.CEL" "GSM362171.CEL" "GSM362175.CEL" "GSM362176.CEL"
[17] "GSM362177.CEL" "GSM362180.CEL" "GSM362181.CEL" "GSM362184.CEL"
[21] "GSM362185.CEL" "GSM362188.CEL" "GSM362189.CEL" "GSM362192.CEL"
[25] "GSM362193.CEL" "GSM362194.CEL" "GSM362197.CEL" "GSM362198.CEL"
[29] "GSM362201.CEL" "GSM362202.CEL" "GSM362203.CEL" "GSM362204.CEL"
[33] "GSM362207.CEL" "GSM362208.CEL" "GSM362211.CEL" "GSM362212.CEL"
[37] "GSM362215.CEL" "GSM362216.CEL" "GSM362217.CEL" "GSM362221.CEL"
[41] "GSM362222.CEL" "GSM362225.CEL" "GSM362226.CEL" "GSM362229.CEL"
[45] "GSM362230.CEL" "GSM362233.CEL" "GSM362234.CEL" "GSM362237.CEL"
[49] "GSM362238.CEL" "GSM362239.CEL" "GSM362240.CEL" "GSM362243.CEL"
[53] "GSM362244.CEL"
data.mo <- ReadAffy (filenames = con.mo, celfile.path="GSE14578_RAW_cel")
pma <- mas5calls data.mo)
gc.nor <- gcrma data.mo, fast = F)
# Keep only probesets present in at least three samples.
ke.mo <- rowSums(exprs(pma) == "P") >= 3
ex.set <- gc.nor[ke.mo, ]
isa.nor <- ISANormalize(ex.set)
set.seed(123)
mo <- ISA(ex.set, flist = NA, thr.gene = 3,thr.cond = c(1, 2), no.seeds = 1000)
Error in get(paste(sep = "", annotation(data), "ENTREZID")) :
object 'ath1121501ENTREZID' not found
And the session information is:
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
locale:
[1] C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] xtable_1.8-2 KEGG.db_3.2.3 GO.db_3.4.0
[4] eisa_1.26.0 isa2_0.3.5 ath1121501probe_2.18.0
[7] gcrma_2.46.0 ath1121501cdf_2.18.0 GOstats_2.40.0
[10] graph_1.52.0 ath1121501.db_3.2.3 org.At.tair.db_3.4.0
[13] Category_2.40.0 Matrix_1.2-8 AnnotationDbi_1.36.2
[16] IRanges_2.8.1 S4Vectors_0.12.1 gplots_3.0.1
[19] ape_4.1 limma_3.30.13 affy_1.52.0
[22] Biobase_2.34.0 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.10 XVector_0.14.0 BiocInstaller_1.24.0
[4] tools_3.3.0 bitops_1.0-6 zlibbioc_1.20.0
[7] digest_0.6.12 annotate_1.52.1 RSQLite_1.1-2
[10] memoise_1.0.0 preprocessCore_1.36.0 nlme_3.1-131
[13] lattice_0.20-34 DBI_0.5-1 genefilter_1.56.0
[16] Biostrings_2.42.1 gtools_3.5.0 caTools_1.17.1
[19] grid_3.3.0 GSEABase_1.36.0 XML_3.98-1.5
[22] RBGL_1.50.0 survival_2.40-1 gdata_2.17.0
[25] splines_3.3.0 AnnotationForge_1.16.0 KernSmooth_2.23-15
[28] RCurl_1.95-4.8 affyio_1.44.0