Hi all,

I'm having a bit of problem with the TxDb.Hsapiens.UCSC.hg19.knownGene, most of the Entrez identifiers I used are fine when I use the function:  transcriptsBy (TxDb.Hsapiens.UCSC.hg19.knownGene, by = "gene")

For example: (example that works) 

------------------------------------------------------------------------------------------------------------------

MYOT <-'9499'

transcriptCoordsByGene.GRangesList.MYOT <-
  transcriptsBy (TxDb.Hsapiens.UCSC.hg19.knownGene, by = "gene") [MYOT]
transcriptCoordsByGene.GRangesList.MYOT
#GRangesList object of length 1:
#$9499 
#GRanges object with 4 ranges and 2 metadata columns:
#seqnames                 ranges strand |     tx_id     tx_name
#<Rle>              <IRanges>  <Rle> | <integer> <character>
#[1]     chr5 [137022410, 137223540]      + |     21288  uc011cye.2
#[2]     chr5 [137203545, 137223540]      + |     21290  uc003lbv.3
#[3]     chr5 [137203545, 137223540]      + |     21291  uc011cyg.2
#[4]     chr5 [137203545, 137223540]      + |     21292  uc011cyh.2

---------------------------------------------------------------------------------------------------

However, for some other genes such as 201625 which is Entrez code for DNAH12 gene in human (I used library(org.Hs.eg.db) and checked with NCBI) I start to get: 

Error: subscript contains out-of-bounds indices

Could you please tell me how I can solve this problem? 

or is there any other packages I can use to extract these genes' data?

I need the data here so that I can analyse the motif using the rGADEM package

I am a medical student and extremely new to R and bioconductor 

my entire set of genes (Entrez identifiers) which I need to analyse are 

 [1]   1002  10233 114798 122481 126792 126820 128344 130827   1428 146845   1493 150483 150572
[14] 159989    183   1852 201625   2167  22824  22885  23676 254956 255101 257177  25992  26576
[27] 266629 283152 283726 285141  29895   3067 340286 340706   3860 387712 389125 389177   4617
[40]   4621   4625  51364   5144  51778   5212  54585  55815  56203  56849  56901  57494   6345
[53]  64102  64446 644890   6588   7042   7060   7138   7273   7322   7337    796  79933   8048
[66]   8091   8125  83450  83657  83894     88  89765   9172   9499

Like I said, some of these work perfectly, others don't.

Any help would be appreciated.

Thank you. 

Entrez Gene IDs, like all other identifiers are not static. Sometimes people realize that two IDs are really pointing to the same thing, and one gets discontinued. This happens on a regular basis (monthly, I believe). The org.Hs.eg.db and TxDb.Hsapiens.UCSC.hg19.knownGene packages were built last year at about the same time, and it's possible that some of the changes in the Gene table at NCBI hadn't yet percolated through whatever table UCSC uses to map Gene IDs to their knownGene IDs.

Anyway, you would do well to first filter your gene IDs to the subset of those that are in the TxDb object, and then you can try to figure out what's up. One possibility is that the IDs are out of sync, in which case you could get the gene_history file from NCBI and then query for the IDs that aren't in the TxDb object to see if there are retired IDs that you could look for in the TxDb object.