[BioC] iffail argument in mget of mas5, rma

[James MacDonald]

You should upgrade to affy 1.4.30, which doesn't have this bug.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Adaikalavan Ramasamy <ramasamy at cancer.org.uk> 05/18/04 01:29PM >>>
I am using R.1.9.0 upgraded to affy 1.4.29, Biobase 1.4.14. I get the
following error below with rma() and mas5() functions and tried to
figure out what is happening all afternoon. I tried it with a couple
of
datasets with the same results. Can anyone help ?

Thank you, Adai.


> library(affy)
Welcome to Bioconductor
         Vignettes contain introductory material.  To view,
         simply type: openVignette()
         For details on reading vignettes, see
         the openVignette help page.
> library(gcrma)
> data <- ReadAffy()
> data
AffyBatch object
size of arrays=536x536 features (134681 kb)
cdf=Hu6800 (7129 affyids)
number of samples=60
number of genes=7129
annotation=hu6800
> print(date())
[1] "Tue May 18 18:16:42 2004"
>
> data.rma <- rma( data )
Error in mget(genenames, pos, envir, iffail = NA) :
        unused argument(s) (iffail ...)

> data1.mas5 <- mas5(data1)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...Error in mget(genenames, pos, envir, iffail =
NA) :
        unused argument(s) (iffail ...)
Execution halted

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