readCel2eSet           package:tilingArray           R Documentation

_R_e_a_d _c_e_l_f_i_l_e_s _i_n_t_o _a_n _E_x_p_r_e_s_s_i_o_n_S_e_t _o_b_j_e_c_t.

_D_e_s_c_r_i_p_t_i_o_n:

     This is a wrapper for 'ReadAffy' that returns an 'ExpressionSet'
     object rather than an AffyBatch. This is particularly usefiles for
     arrays for which we have or need no CDF environment.

_U_s_a_g_e:

     readCel2eSet(filename, adf, path=".", rotated=FALSE, ...)

_A_r_g_u_m_e_n_t_s:

filename: Character vector with CEL file names. Either 'filename' or
          'adf' need to be specified, but not both.

     adf: Object of class 'AnnotatedDataFrame'.

    path: Character scalar with path to CEL files.

 rotated: Logical scalar, see details.

     ...: Further arguments that are passed on to
          'new("ExpressionSet")'.

_D_e_t_a_i_l_s:

     The 'rotate' options allows to deal with different versions of the
     scanner software. Older versions rotated the image by 90 degrees,
     newer ones do not. Use the default 'rotated=FALSE' for CEL files
     produced by the newer version.

_V_a_l_u_e:

     'ExpressionSet' object.

_A_u_t_h_o_r(_s):

     W. Huber

_E_x_a_m_p_l_e_s:

     ## To test the rotation, look at the scatterplot between two DNA hybes
     ## that were measured with scanner software that rotated (041120) and did
     ## not rotate (060125)
     ##
     ## cp /ebi/research/huber/Projects/tilingArray/Celfiles/041120_S96genDNA_re-hybe.cel.gz ~/p/tmp
     ## cp /ebi/research/huber/Projects/allelicTranscription/celfiles_allelictrans/060125_S96_genomicDNA.zip ~/p/tmp
     ## cd ~/p/tmp
     ## gunzip 041120_S96genDNA_re-hybe.cel.gz
     ## unzip 060125_S96_genomicDNA.zip
     ##
     ## Not run: 
     library("affy")
     options(error=recover)

     e1 = readCel2eSet("041120_S96genDNA_re-hybe.cel", rotated=TRUE)
     e2 = readCel2eSet("060125_S96_genomicDNA.CEL")

     smoothScatter(log(exprs(e1)), log(exprs(e2)), nrpoints=0)
     ## End(Not run)

