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Question: Why are important organisms missing from AnnotationHub. Example query(hub, "Zea")
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gravatar for slbai01
7 days ago by
slbai010
slbai010 wrote:

I used the latest database, but the data obtained than the old database, the lack of exactly what I want.

As follows, I use the  "AnnotationHub(), query(hub,'zea') " function to get the results shown in the left, but I get the result is the right look, the lack of 'AH55736' is exactly what I want.

Then I try to change the "snapshotDate()" date, but still do not get the desired result. As follow:

Then I follow the tutorial in the official document, the results are still missing a lot, as shown below, the tutorial got 940 results, but I only got 79 results.

This is my question and look forward to your answer.

 

Thank you. 

ADD COMMENTlink modified 7 days ago • written 7 days ago by slbai010

You are being needlessly cryptic. You don't say what the 'desired result' is, except to say that you didn't get it. What is clear is that you didn't get what you want; what is not clear is what that might be. And what are we supposed to infer from the screenshots with the red boxes?

ADD REPLYlink written 7 days ago by James W. MacDonald44k

Sorry,I have re-described the problem and looked forward to your answer.

ADD REPLYlink written 7 days ago by slbai010

Which is your session info? Did you check if you have all the packages (and R) up to date?

ADD REPLYlink written 6 days ago by Lluís R270

This is my session info, They are all up to date.

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
[1] AnnotationHub_2.2.5 BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10                 IRanges_2.4.8                digest_0.6.12               
 [4] mime_0.5                     R6_2.2.2                     xtable_1.8-2                
 [7] DBI_0.7                      stats4_3.2.2                 RSQLite_1.1-2               
[10] BiocInstaller_1.20.3         httr_1.2.1                   S4Vectors_0.8.11            
[13] tools_3.2.2                  Biobase_2.30.0               shiny_1.0.3                 
[16] httpuv_1.3.3                 AnnotationDbi_1.32.3         memoise_1.1.0               
[19] htmltools_0.3.5              interactiveDisplayBase_1.8.0
ADD REPLYlink written 6 days ago by slbai010

You are using R version 3.2.2. The most up to date version of R (and Bioconductor examples you posted are from that version) is 3.4. Update R and the bioconductor packages and check again if there are the same errors. For instance Biobase version number is 2.36.2 and you are using version 2.30.0 which is 3 years old.

ADD REPLYlink written 6 days ago by Lluís R270

Thank you !

I downloaded the latest version of the R software and used the latest package, my problem solved.

ADD REPLYlink written 6 days ago by slbai010
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