I didn't get any attached data, but my suspicion here is that you have somehow
got RefSeq IDs in column 8 of human, as well as the gene symbols. Did you read
this data in from a text file?
Eleni Christodoulou wrote:
An example is:
symbol=human[which(human[,3] %in% genes.sam.names),8]
The data* human* and *genes.sam.names* are attached. The result of the above
command is:
symbol
[1] CCL18 MARCO SYT13
[4] FOXC1 CDH3
[7] CA12 CELSR1 NM_018440
[10] MICROTUBULE-ASSOCIATED NM_015529 ESR1
[13] PHGDH GABRP LGMN
[16] MMP9 BMP7 KLF5
[19] RIPK2 GATA3 NM_032023
[22] TRIM2 CCND1 MMP12
[25] LDHB AF493978 SOD2
[28] SOD2 SOD2 NME5
[31] STC2 RBP1 ROPN1
[34] RDH10 KRTHB1 SLPI
[37] BBOX1 FOXA1 NM_005669
[40] MCCC2 CHI3L1 GSTM3
[43] LPIN1 DSC2 FADS2
[46] ELF5 CYP1B1 LMO4
[49] AL035297 NM_152398 AB018342
[52] PIK3R1 NFKBIE MLZE
[55] NFIB NM_052997 NM_006023
[58] CPB1 CXCL13 CBR3
[61] NM_017527 FABP7 DACH
[64] IFI27 ACOX2 CXCL11
[67] UGP2 CLDN4 M12740
[70] IGKC IGKC CLECSF12
[73] AY069977 HOXB2 SOX11
[76] NM_017422 TLR2
[79] CKS1B BC017946 APOBEC3B
[82] HLA-DRB1 HLA-DQB1
[85] CCL13 C4orf7
[88] NM_173552
21345 Levels: (2 (32 (55.11 (AIB-1) (ALU (CAK1) (CAP4) (CASPASE ... ZYX
As you can see, apart from gene symbols, which is the required thing, RefSeq
ID sare also retrieved...
Thanks a lot,
Eleni
On Fri, Jun 6, 2008 at 1:23 PM, Dieter Menne <[EMAIL PROTECTED]>
wrote:
Eleni Christodoulou <elenichri <at> gmail.com> writes:
I was trying to select a column of a data frame using the *which*
command. I
was actually selecting the rows of the data frame using *which, *and then
displayed a certain column of it. The command that I was using is:
sequence=*mydata*[*which*(human[,3] %in% genes.sam.names),*9*]
....
Please provide a running example. The *mydata* are difficult to read.
Dieter
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