file' must be a character string or connection Error
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!
1 answer
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
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