file' must be a character string or connection Error

Question

[bio94]

I get this error whenever I try to perform this operation in the CRISclassifier package in R and I am not sure on how to rectify the same.

 > cris_classifier(input.exp.filename = new, output.name="cris", nresmpl=1000)
    Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
      'file' must be a character string or connection



 > head(new)
      symbol GSM358387 GSM358392 GSM358395 GSM358396 GSM358397 GSM358399 GSM358401 GSM358406 GSM358414 GSM358415 GSM358417
    1 MT-ND1 11.004360 10.692454 11.028146 11.258794 11.039005 11.167989 11.478223 11.321304 11.586453 10.856381 10.955958
    2  MT-TI  8.469522  8.473875  8.476619  8.446452  7.875122  7.725043  8.282674  8.615612  8.690866  8.191190  8.599000
    3  MT-TM  6.976623  7.209450  7.719266  6.815779  6.957543  7.753237  7.060063  7.326970  7.483037  7.360345  7.567729
    4 MT-ND2  9.590917  9.307784  9.626519  9.310110  9.268624  9.284609  9.424225  9.418507  9.537481  9.480964  9.588074
    5 MT-CO1  4.504853  4.668074  4.636719  4.438557  4.519769  4.416414  4.518444  4.425952  4.497750  4.899380  4.529719
      GSM358419 GSM358420 GSM358429 GSM358430 GSM358433 GSM358437 GSM358441 GSM358447 GSM358469 GSM358474 GSM358477
    1 10.918676 11.303386 10.726991 11.447482 11.277053 11.408520 11.449815 10.338640 11.382200 11.331540 10.750465
    2  8.475890  8.230981  8.041038  8.321014  9.331570  8.388808  8.549037  8.456947  8.483367  8.800022  8.597835
    3  7.671317  6.998998  7.202345  7.297212  6.937482  6.879666  8.256243  7.824174  7.730995  6.957210  7.840316
    4  9.574755  9.255486  9.250306  9.635944  9.291210  9.186388  9.524402  9.047276  9.305240  9.091134  9.122343
    5  4.527993  4.556324  4.547750  4.560562  4.670047  4.423828  4.693070  4.746445  4.591236  4.616007  4.840607...

Would appreciate any help in this regard.Many thanks!

Answer 1

[Mark]

Don't name your dataframes/objects the same as function names. new is a function. While R has powerful scoping rules, sometimes it has trouble. It's best just to avoid calling any object the same as a function name.

Reload your data and assign it a proper descriptive name. eg: koala_dat

[bio94]

Sure. Thanks very much.

[Mark]

upvote so I can get this limiter off.