[BioC] help with matrix

[James W. MacDonald]

Hi Alberto,

Alberto Goldoni wrote:
> Dear All,
> if i have a dataframe "b" like this one:
>                        SHR1             SHR2         SHR3          WK1
>          WK2
> 1368290_at        7.680187      7.214491    7.156308    7.064027     4.496945
> 1368637_at       11.393928     11.337781   11.420565   11.464711     9.329639
> 1369202_at        7.766468      7.910206    7.553126    7.559352     4.169429
> 1370463_x_at      8.896523      8.865356    8.847850    8.830867     6.388185
> 1370806_at        9.754578      9.752164    9.718223    9.680127    11.756575
> 1370815_at        5.781366      5.799394    5.815935    5.847172     4.318191
> 1371033_at        5.063421      4.303661    4.598223    4.506666     8.297466
> 1371137_at        8.010640      7.737443    7.625425    7.629711     4.105173
> 1371960_at        7.293301      7.149758    6.960322    7.075571     9.944016
> 1372120_at        6.300269      6.252419    6.296085    6.219186     4.747452
> 
> and i would like to obtain another dataframe like this:
> 
>    GeneID     SHR1      SHR2   SHR3          WK1          WK2
> 1     374  5.068725  4.833424  5.251337  9.105219  9.384213
> 2    2289  7.764840  7.842467  7.973488 11.285194 11.189364
> 3   10563  4.824265  4.780033  4.417243  8.362088  7.825695
> 4     687  4.607949  5.169052  4.947950  7.463272  7.370329
> 5   80149  7.729777  7.472989  7.617576 10.281806  9.541200
> 6    5033  9.111025  8.239996  8.677078 11.213525 10.343982
> 7    7088  5.782532  6.094321  6.069819  8.451878  8.442783
> 8   64764  9.669172  9.684598  9.922658 11.298087 11.198835
> 9   10628 10.555573 10.461917 11.067293 12.686023 12.624490
> 10   5087  8.535518  8.652258  8.576578 10.263172  9.893716
> 
> so the questions are:
> 1) how can i get the first colon (1,2,3......10)
> 2) how can i substitute the affyID with the GeneID
> 3) how can assembly the 1) and 2) columns in the first dataframe in
> order to obtain the second one.

The first column in your data.frame 'b' isn't a column - it's the 
row.names for the data.frame. Note that you don't give us much to go on, 
like the fact that you are using a rat2302 chip. A complete description 
of the problem will go far to help those who might help you.

I will ignore questions 1 and 3 because I have no idea what you are 
asking for.

 > suppressMessages(library(rat2302.db))
 > d <- data.frame(GeneID = unlist(mget(row.names(b), rat2302ENTREZID)), b)
 > d
              GeneID      SHR1      SHR2      SHR3       WK1       WK2
1368290_at    83476  7.680187  7.214491  7.156308  7.064027  4.496945
1368637_at    64171 11.393928 11.337781 11.420565 11.464711  9.329639
1369202_at   286918  7.766468  7.910206  7.553126  7.559352  4.169429
1370463_x_at 414819  8.896523  8.865356  8.847850  8.830867  6.388185
1370806_at   246298  9.754578  9.752164  9.718223  9.680127 11.756575
1370815_at    24587  5.781366  5.799394  5.815935  5.847172  4.318191
1371033_at   309622  5.063421  4.303661  4.598223  4.506666  8.297466
1371137_at   252898  8.010640  7.737443  7.625425  7.629711  4.105173
1371960_at   313053  7.293301  7.149758  6.960322  7.075571  9.944016
1372120_at   300968  6.300269  6.252419  6.296085  6.219186  4.747452

If you really want to exchange your Affy IDs with numbers, see 
?row.names. In addition, if you are really struggling with such simple 
data manipulation steps, you need to read (at the very least) 'An 
Introduction to R'. You can find that at the R home page, or by simply 
googling it.

Best,

Jim


> 
> best regards
> 
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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