Question: Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
1
gravatar for Rinaldo Bertossa
3.5 years ago by
Netherlands
Rinaldo Bertossa20 wrote:

Hi,

I've performed a DE genes analysis with edgeR.

Now I am trying to analyze GO terms associated with my DE genes.

I'm trying to get the GO terms for my 'non-model organism' via the AnnotationHub.

I'm trying to follow these instructions (given in the post https://support.bioconductor.org/p/76482/#77483):

library(AnnotationHub)
hub = AnnotationHub()
org.Cg.eg.db <- hub[["AH48061"]]
gene.go <- select(org.Cg.eg.db, keys(org.Cg.eg.db), "GOALL")
library(GO.db)
go.names <- select(GO.db, keys(GO.db), "TERM")
k <- kegga(fit, gene.pathway=gene.go, pathway.names=go.names)
topKEGG(k)

Up to a certain point it seems to work, then I keep getting the error:

Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes

I could not find anything related to what I'm doing that helps me solving this.

Here below is what I've tried and the result. On the bottom I've added traceback() and sessionInfo().

Thanks for any advice.

 

> library(AnnotationHub)
> hub = AnnotationHub()
snapshotDate(): 2016-03-09
> org.Nv.eg.db <- hub[["AH48280"]]
loading from cache ‘C:/Users/Rinaldo C. Bertossa/Documents/AppData/.AnnotationHub/54586’
> columns(org.Nv.eg.db)
[1] "ACCNUM"      "ALIAS"       "CHR"         "ENTREZID"    "EVIDENCE"    "EVIDENCEALL" "GENENAME"  
[8] "GID"         "GO"          "GOALL"       "ONTOLOGY"    "ONTOLOGYALL" "PMID"        "PROBEID"   
[15] "REFSEQ"      "SYMBOL"
> head(keys(org.Nv.eg.db))
Error in head(keys(org.Nv.eg.db)) :
  error in evaluating the argument 'x' in selecting a method for function 'head': Error in sqliteSendQuery(conn, statement) :
  error in statement: no such table: c.probes
> gene.go <- select(org.Nv.eg.db, keys(org.Nv.eg.db), "GOALL")
Error in sqliteSendQuery(conn, statement) :
  error in statement: no such table: c.probes

> traceback()
22: .Call(rsqlite_query_send, con@Id, as.character(statement), bind.data)
21: sqliteSendQuery(conn, statement)
20: .local(conn, statement, ...)
19: dbSendQuery(conn, paste("SELECT * FROM ", name, "LIMIT 1"))
18: dbSendQuery(conn, paste("SELECT * FROM ", name, "LIMIT 1"))
17: .local(conn, name, ...)
16: FUN(X[[i]], ...)
15: FUN(X[[i]], ...)
14: lapply(X = X, FUN = FUN, ...)
13: sapply(tables, FUN = dbListFields, con = con)
12: sapply(tables, FUN = dbListFields, con = con)
11: .deriveTableNameFromField(field = keytype, x)
10: .noSchemaKeys(x, keytype)
9: .keys(x, keytype)
8: smartKeys(x = x, keytype = keytype, ..., FUN = .keys)
7: keys(org.Nv.eg.db)
6: keys(org.Nv.eg.db)
5: .testForValidKeys(x, keys, keytype, fks)
4: .testSelectArgs(x, keys = keys, cols = cols, keytype = keytype,
       fks = fks, skipValidKeysTest = skipValidKeysTest)
3: .select(x, keys, columns, keytype, jointype = jointype, ...)
2: select(org.Nv.eg.db, keys(org.Nv.eg.db), "GOALL")
1: select(org.Nv.eg.db, keys(org.Nv.eg.db), "GOALL")

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252  
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] shiny_0.13.1         org.Hs.eg.db_3.2.3   GO.db_3.2.2          RSQLite_1.0.0        DBI_0.3.1          
[6] AnnotationDbi_1.32.3 IRanges_2.4.8        S4Vectors_0.8.11     Biobase_2.30.0       edgeR_3.12.0       
[11] limma_3.26.8         AnnotationHub_2.2.5  BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
[1] Rcpp_0.12.3                  splines_3.2.3                statmod_1.4.24             
[4] xtable_1.8-2                 lattice_0.20-33              R6_2.1.2                   
[7] httr_1.1.0                   tools_3.2.3                  grid_3.2.3                 
[10] htmltools_0.3                digest_0.6.9                 interactiveDisplayBase_1.8.0
[13] codetools_0.2-14             curl_0.9.6                   mime_0.4                   
[16] BiocInstaller_1.20.1         locfit_1.5-9.1               jsonlite_0.9.19            
[19] httpuv_1.3.3  
ADD COMMENTlink modified 3.2 years ago by cagenet3420 • written 3.5 years ago by Rinaldo Bertossa20
1

One unusual thing here are the spaces in the file path. You could try copying the resource C:/Users/Rinaldo C. Bertossa/Documents/AppData/.AnnotationHub/54586 to a location without a space, e.g., c:/Temp/, and try org.Nv.eg.db <- AnnotationDbi::loadDb("c:/Temp/54586").

 

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Martin Morgan ♦♦ 23k
1

Path spaces are probably not the problem.

> hub2 <- AnnotationHub(cache = "C:/New folder/")
updating AnnotationHub metadata: retrieving 1 resource
  |======================================================================| 100%
snapshotDate(): 2016-03-09
Warning message:
In dir.create(cache, recursive = TRUE) : 'C:\New folder' already exists
> org.Nv2.eg.db <- hub2[["AH48280"]]
loading from cache 'C:/New folder//54586'
> head(keys(org.Nv2.eg.db))
[1] "100101930" "100101931" "100102554" "100104006" "100104126" "100107367"
> gene.go <- select(org.Nv2.eg.db, keys(org.Nv2.eg.db), "GOALL")
'select()' returned 1:many mapping between keys and columns
ADD REPLYlink written 3.5 years ago by James W. MacDonald51k

Hi Martin, thank you. I'm not familiar with SQL yet. I get this error when I try running your code (after having copied the resource): Error: is(x, "AnnotationHub") is not TRUE 

ADD REPLYlink written 3.5 years ago by Rinaldo Bertossa20
1

My bad, I updated the instruction to org.Nv.eg.db <- AnnotationDbi::loadDb("c:/Temp/54586"). As Jim shows spaces are probably not the problem, but it could still be something about the particular path (though this also sounds unlikely given that you clarify that it is just keys() that causes problems)...

ADD REPLYlink written 3.5 years ago by Martin Morgan ♦♦ 23k
Answer: Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.
1
gravatar for James W. MacDonald
3.5 years ago by
United States
James W. MacDonald51k wrote:

Not sure how much help this will be, but I can't replicate, and I don't see anything obviously wrong with your Bioc install:

> hub <- AnnotationHub()
snapshotDate(): 2016-03-09
> org.Nv.eg.db <- hub[["AH48280"]]

> head(keys(org.Nv.eg.db))
[1] "100101930" "100101931" "100102554" "100104006" "100104126" "100107367"
> gene.go <- select(org.Nv.eg.db, keys(org.Nv.eg.db), "GOALL")
'select()' returned 1:many mapping between keys and columns
> 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=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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] AnnotationDbi_1.32.3 IRanges_2.4.6        S4Vectors_0.8.11    
[4] Biobase_2.30.0       AnnotationHub_2.2.3  BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3                  digest_0.6.9                
 [3] mime_0.4                     R6_2.1.2                    
 [5] xtable_1.8-0                 DBI_0.3.1                   
 [7] RSQLite_1.0.0                BiocInstaller_1.20.1        
 [9] httr_1.1.0                   curl_0.9.5                  
[11] tools_3.2.2                  shiny_0.13.0                
[13] httpuv_1.3.3                 compiler_3.2.2              
[15] htmltools_0.3                interactiveDisplayBase_1.8.0
>
ADD COMMENTlink written 3.5 years ago by James W. MacDonald51k

Thank you James, I appreciate. At least I know it should work ;)

 

ADD REPLYlink written 3.5 years ago by Rinaldo Bertossa20

I've downloaded two other databases and tried again but I get the same error. For all I can use e.g. columns() but not keys(). So I would exclude a problem with the database itself...

ADD REPLYlink written 3.5 years ago by Rinaldo Bertossa20

Could that help: my personal libraries (including AnnotationHub, AnnotationDBI) are on Dropbox. This allows me to access them from work and home without the need to install and update them twice. Standard R libraries are local.

Update: I stored personal libraries locally. It did not solve the problem.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Rinaldo Bertossa20
Answer: Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.
1
gravatar for Rinaldo Bertossa
3.5 years ago by
Netherlands
Rinaldo Bertossa20 wrote:

I think I found the problem or, better, the solution.

There seems to be an incompatibility between the DGElist object called 'y' created in edgeR and calling the AnnotationHub/AnnotationDBI commands above (e.g. head(keys(org.Nv.eg.db)) ), which results in an error (in my hands at least).

The solution is to give the DGElist object a different name than 'y'. Then the commands above work fine.

This is how I solved the problem. Why assigning 'y' to the DGElist object causes the incompatibility with, I guess, AnnotationHub/AnnotationDBI I do not know.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Rinaldo Bertossa20
Answer: Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.
1
gravatar for cagenet34
3.2 years ago by
cagenet3420
Toulouse, France, INRA
cagenet3420 wrote:

Hi Rinaldo,

I also had the same error and your tip works. I change my DGElist object name from "y" to "resDGE" and now it's ok.

Thank you for your solution.

Carine

ADD COMMENTlink written 3.2 years ago by cagenet3420

This helped to identify the problem, which is fixed in AnnotationDbi version 1.34.4 / 1.35.4; these should be available in a couple of days. Thanks for your help and patience.

ADD REPLYlink written 3.2 years ago by Martin Morgan ♦♦ 23k
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