Hi, Jim:
Thanks for debugging for me!
I tried the following commands and got exactly what you have expected.
Also, I tried everything in the unix system, and got exactly the same
error message.
Wenqiong
-----Original Message-----
From: James W. MacDonald [mailto:jmacdon@med.umich.edu]
Sent: Tuesday, March 29, 2005 12:14 PM
To: Wenqiong Chen
Cc: Bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] gcrma problem
What happens if you do:
library(disdiv712aprobe)
data.frame(disdiv712aprobe)[1:10,]
You should get something like:
sequence x y Probe.Set.Name
Probe.Interrogation.Position Target.Strandedness
1 CACCCAGCTGGTCCTGTGGATGGGA 718 317 1007_s_at
3330 Antisense
2 GCCCCACTGGACAACACTGATTCCT 1105 483 1007_s_at
3443 Antisense
3 TGGACCCCACTGGCTGAGAATCTGG 584 901 1007_s_at
3512 Antisense
4 AAATGTTTCCTTGTGCCTGCTCCTG 192 205 1007_s_at
3563 Antisense
5 TCCTTGTGCCTGCTCCTGTACTTGT 844 979 1007_s_at
3570 Antisense
6 TGCCTGCTCCTGTACTTGTCCTCAG 537 971 1007_s_at
3576 Antisense
7 TCCTGTACTTGTCCTCAGCTTGGGC 748 983 1007_s_at
3583 Antisense
8 ACTTGTCCTCAGCTTGGGCTTCTTC 1119 177 1007_s_at
3589 Antisense
9 TCCTCCATCACCTGAAACACTGGAC 504 983 1007_s_at
3615 Antisense
10 AAGCCTATACGTTTCTGTGGAGTAA 624 245 1007_s_at
3713 Antisense
>
How about
library(disdiv712acdf)
get(ls(disdiv712acdf), disdiv712acdf)
You should get something like:
pm mm
[1,] 369707 370871
[2,] 563318 564482
[3,] 1049349 1050513
[4,] 238813 239977
[5,] 1140401 1141565
[6,] 1130782 1131946
[7,] 1144961 1146125
[8,] 207148 208312
[9,] 1144717 1145881
[10,] 285805 286969
[11,] 1351879 1353043
[12,] 1170814 1171978
[13,] 906807 907971
[14,] 547053 548217
[15,] 1221909 1223073
[16,] 27611 28775
Wenqiong Chen wrote:
> This is something which frustrates me again!
> Yes, I did do "R CMD INSTALL" from the dos command line, and I can
clearly see that the package is in the R library.
> Regarding the naming issue, I did not specify anything. Right now,
the
two packages I built in the library is "disdiv712acdf", and
"disdiv712aprobe". Looks pretty consistent.
> There is clearly something not trivial there which caused the
problem,
maybe related to my computer? I am going to give a try in the unix
system and see what happens.
> Thanks a lot for your help!
> Wenqiong
>
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon@med.umich.edu]
> Sent: Tuesday, March 29, 2005 11:38 AM
> To: Wenqiong Chen
> Cc: Bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] gcrma problem
>
> Wenqiong Chen wrote:
>
>>O.K, here is the step where the error started to occur when I run
the
>>content of the function "compute.affinities".. "
>>
>>
>>>getProbePackage(probepackagename)
>>
>>[1] "Checking to see if your internet connection works..." Error in
>>install.packages2(probepackage, lib = lib) : recursive default
>>argument reference " Alternatively, when I use:
>>
>>
>>>getProbePackage(disdiv712aprobe) #disdiv712aprobe is
the
>>>probepackagename
>>
>>Warning messages: 1: the condition has length > 1 and only the first
>>element will be used in: if (package %in% c("ctest", "eda",
"modreg",
>>"mva", "nls", "stepfun", 2: the condition has length > 1 and only
the
>>first element will be used in: if (package == "mle") { 3: the
>>condition has length > 1 and only the first element will be used in:
>>if (package == "lqs") { [1] "Checking to see if your internet
>>connection works..." Note: You did not specify a download type.
>>Using a default value of: Win32 This will be fine for almost all
users
>>
>>Error in FUN(X[[2]], ...) : Malformed 'pkgs' parameter " I also
>>noticed that when I execute this line, it attempts to download
>>something from BioConductor.
>>
>>As Jim already realized, this is not a public GeneChip, but did
adopt
>>a standard Affy design. I made the cdf and probe packages by myself
>>using the functions in BioConductor. The R version I am using is
>>R2.0.1, the gcrma package is from the BioConductor 1.5 release.
>
>
> The function getProbePackage() is trying to download the probe
package
from the BioC website because it thinks the correct one is not
installed. When you made the cdf and probe packages yourself, did you
specify a name for either? If so, this may be the cause of the
problem.
>
> In addition, after making the packages, did you install them using R
CMD INSTALL? If you didn't install them, then they will not be
available
for R to use, which is another possibility.
>
> If you are on a *nix machine, installing should be straightforward.
If
you are on MacOS or Windows, you may need to get some tools. If so,
you
will need to see the corresponding FAQ on the R-project website.
>
> HTH,
>
> 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
>
>
>
>
>
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--
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
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