I attempted to use KEGGprofile's convertId() to get my RNA-seq counts into NCBI gene IDs. I think the genes were given to me in mgi_symbol format. After running convertId() I revived the warning message, repeated until warnings() maxed out:
1: In FUN(newX[, i], ...) : NAs introduced by coercion
I was very concerned by this because I was afraid a substantial portion of my data was now NA. This said I have had trouble tracking them down. (That said the genes that appear in the header all seem to be converted properly.) Still I wanted to find the NAs.
I tried:
> with_id[is.na(with_id[, "X"])]
which returns:
character(0)
I also tried:
>matmain <- is.na(with_id)
>which(matmain, arr.ind = TRUE)
but that just returned:
row col
Any advice for figuring out where they have disappeared too?
Here are a the first few rows of my converted matrix:
X USC_1 USC_2 USC_3 USC_NDT_1 USC_3DT_1
100009600 "Zglp1" "1.167246e+00" "1.314248e+00" "1.414709e-01" "2.111822e-01" "3.060517e-01"
100009609 "Vmn2r65" "0.000000e+00" "0.000000e+00" "0.000000e+00" "0.000000e+00" "0.000000e+00"
100009614 "Gm10024" "0.000000e+00" "0.000000e+00" "0.000000e+00" "0.000000e+00" "6.987166e-02"
100012 "Oog3" "0.000000e+00" "0.000000e+00" "0.000000e+00" "0.000000e+00" "4.143595e-02"
100017 "Ldlrap1" "1.153021e+01" "1.048102e+01" "1.175961e+01" "6.312788e+00" "1.315837e+01"
100019 "Mdn1" "2.269278e+00" "1.780199e+00" "3.189900e+00" "1.276779e+00" "2.080692e+00"
100034251 "Wfdc17" "0.000000e+00" "0.000000e+00" "0.000000e+00" "0.000000e+00" "0.000000e+00"
100034361 "Mfap1b" "2.980608e+01" "2.990117e+01" "2.839012e+01" "2.375291e+01" "3.852410e+01"
(Oddly it also gained 275 rows according to dim())
On a vaguely related note I was hoping to get another pair of eyes on my filter of choice, I thought that these fell in the "mgi_symbol" mart filter (for "mmusculus_gene_ensembl") but I am not sure. Some of my gene identifiers:
[571] "A830031A19Rik" "A830080D01Rik" "A930002H24Rik" "A930003A15Rik" "A930004D18Rik" "A930009A15Rik"
[577] "A930017K11Rik" "A930018M24Rik" "A930018P22Rik" "A930033H14Rik" "AA467197" "AA792892"
[583] "AA986860" "Aaas" "Aacs" "Aadac" "Aadacl2" "Aadacl3"
[589] "Aadacl4" "Aadat" "Aaed1" "Aagab" "Aak1" "Aamdc"
[595] "Aamp" "Aanat" "Aar2" "Aard" "Aars" "Aars2"
[601] "Aarsd1" "Aasdh" "Aasdhppt" "Aass" "Aatf" "Aatk"
[607] "AB124611" "Abat" "Abca1" "Abca12" "Abca13" "Abca14"
Thanks for the help!
