[BioC] Affy 1.5.8 functions not working on Mac OS X 10.3
Chad Wayne
cwayne at bcm.tmc.edu
Tue Jan 25 22:43:51 CET 2005
My entire session follows. The previous .RData session was performed on
another computer while I was learning the basics of R and affy. Prior
to loading "timecourse.Rdata", I started X11 and changed the working
directory to the proper working directory with my data in it.
> load("/xxx/xxx/ArrayAnalysis/timecourse.RData")
> ls()
[1] "PMA.Calls" "Pearson.cor" "adjp" "coc.phenodata"
[5] "deg" "eset" "mynova.full" "procs"
[9] "raw" "raw.pvalue" "res" "timecourse"
[13] "x"
> library(affy)
Loading required package: Biobase
Loading required package: tools
Loading required package: reposTools
## Note here that everything loaded just fine, as far as I can tell.
Knowing that these next two functions haven't worked for me, I used
them first.
> pData(eset)
Error: couldn't find function "pData"
> ReadAffy(widget=T)
Loading required package: tkWidgets
Loading required package: widgetTools
Loading required package: tcltk
Loading required package: DynDoc
Error in AllButCelsForReadAffy(..., filenames = filenames, widget =
widget, :
couldn't find function "read.phenoData"
## When I performed ReadAffy(widget=T), the widget did function
normally. I selected the .cel files I wanted use (the ones that made up
the eset above) and then after selecting them, the error message popped
up.
> packageDescription("affy", field="Version")
[1] "1.5.8"
> version
_
platform powerpc-apple-darwin6.8
arch powerpc
os darwin6.8
system powerpc, darwin6.8
status
major 2
minor 0.1
year 2004
month 11
day 15
language R
## This search demonstrates the packages that are active at this point
in the session.
> search()
[1] ".GlobalEnv" "package:tkWidgets" "package:DynDoc"
[4] "package:widgetTools" "package:tcltk" "package:affy"
[7] "package:reposTools" "package:Biobase" "package:tools"
[10] "package:methods" "package:stats" "package:graphics"
[13] "package:grDevices" "package:utils" "package:datasets"
[16] "Autoloads" "package:base"
## I wanted to demonstrate the functions and files associated with affy
in my library. There are 116 of them.
> ls("package:affy")
[1] "$.AffyBatch"
[2] "AffyRNAdeg"
[3] "AllButCelsForReadAffy"
[4] "MAplot"
[5] "Mbox"
[6] "ReadAffy"
[7] "affy.scalevalue.exprSet"
[8] "avdiff"
[9] "barplot"
[10] "barplot.ProbeSet"
[11] "bg.adjust"
[12] "bg.correct"
[13] "bg.correct.mas"
[14] "bg.correct.none"
[15] "bg.correct.rma"
[16] "bg.correct.rma2"
[17] "bg.parameters"
[18] "bgcorrect.methods"
[19] "boxplot"
[20] "cdfFromBioC"
[21] "cdfFromData"
[22] "cdfFromEnvironment"
[23] "cdfFromLibPath"
[24] "cdfName"
[25] "cleancdfname"
[26] "close"
[27] "colnames"
[28] "computeExprSet"
[29] "debug.affy123"
[30] "express.summary.stat"
[31] "express.summary.stat.methods"
[32] "expresso"
[33] "expressoWidget"
[34] "fit.li.wong"
[35] "generateExprSet.methods"
[36] "generateExprVal.method.avgdiff"
[37] "generateExprVal.method.liwong"
[38] "generateExprVal.method.mas"
[39] "generateExprVal.method.medianpolish"
[40] "generateExprVal.method.playerout"
[41] "getCdfInfo"
[42] "hist"
[43] "hlog"
[44] "image"
[45] "indexProbes"
[46] "indices2xy"
[47] "intensity"
[48] "intensity<-"
[49] "just.rma"
[50] "justRMA"
[51] "li.wong"
[52] "list.celfiles"
[53] "loess.normalize"
[54] "ma.plot"
[55] "maffy.normalize"
[56] "maffy.subset"
[57] "mas5"
[58] "mas5.detection"
[59] "mas5calls"
[60] "mas5calls.AffyBatch"
[61] "mas5calls.ProbeSet"
[62] "medianpolish"
[63] "merge.AffyBatch"
[64] "mm"
[65] "mm<-"
[66] "mmindex"
[67] "multiloess"
[68] "mva.pairs"
[69] "ncol"
[70] "normalize"
[71] "normalize.AffyBatch.constant"
[72] "normalize.AffyBatch.contrasts"
[73] "normalize.AffyBatch.invariantset"
[74] "normalize.AffyBatch.loess"
[75] "normalize.AffyBatch.methods"
[76] "normalize.AffyBatch.qspline"
[77] "normalize.AffyBatch.quantiles"
[78] "normalize.AffyBatch.quantiles.robust"
[79] "normalize.constant"
[80] "normalize.invariantset"
[81] "normalize.loess"
[82] "normalize.methods"
[83] "normalize.qspline"
[84] "normalize.quantiles"
[85] "normalize.quantiles.robust"
[86] "nrow"
[87] "open"
[88] "pairs.AffyBatch"
[89] "playerout.costfunction"
[90] "plot.ProbeSet"
[91] "plotAffyRNAdeg"
[92] "plotDensity"
[93] "plotDensity.AffyBatch"
[94] "plotLocation"
[95] "pm"
[96] "pm<-"
[97] "pmcorrect.mas"
[98] "pmcorrect.methods"
[99] "pmcorrect.pmonly"
[100] "pmcorrect.subtractmm"
[101] "pmindex"
[102] "ppset.ttest"
[103] "ppsetApply"
[104] "probeNames"
[105] "probes"
[106] "probeset"
[107] "read.affybatch"
[108] "read.probematrix"
[109] "rma"
[110] "simplemultiLoess"
[111] "summaryAffyRNAdeg"
[112] "tukey.biweight"
[113] "tukeybiweight"
[114] "update"
[115] "whatcdf"
[116] "xy2indices"
## I next performed the capabilities function. The only thing not
available to me was GNOME
> capabilities()
jpeg png tcltk X11 GNOME libz http/ftp sockets
TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE
libxml fifo cledit IEEE754 bzip2 PCRE
TRUE TRUE TRUE TRUE TRUE TRUE
## I finally checked the library path for the R.framework. This is what
I expected. I also physically checked the file heirarchy to make sure
that in "library" there were files for R to use. There are.
> .libPaths()
[1] "/Library/Frameworks/R.framework/Resources/library"
## If I type in eset, rather than getting an expression set matrix (?),
I get the full list of the gene IDs + log values of the samples (45K+
rows)
> eset
list()
attr(,"exprs")
0h-1.cel 0h-2.cel 16h-1.cel 16h-2.cel
1415670_at 10.783245 10.696067 11.372607 11.203421
1415671_at 10.655126 10.972694 11.253215 11.287455
... etc.
## Also wanted to look at the attributes of the phenodata from the
previous session to see whether the session was corrupted.
> coc.phenodata
list()
attr(,"pData")
time.after.hCG
0h-1.cel 0
0h-2.cel 0
16h-1.cel 16
16h-2.cel 16
8h-1.cel 8
8h-2.cel 8
attr(,"varLabels")
attr(,"varLabels")$"time after hCG"
[1] ""
attr(,"class")
[1] "phenoData"
attr(,"class")attr(,"package")
[1] "Biobase"
## Here we see another function error such that affy (BioC?) can't find
the proper cdf file to compare the data against.
> raw
Error in cdfFromBioC(cdfname, cur$where, verbose) :
couldn't find function "testBioCConnection"
AffyBatch object
size of arrays=1002x1002 features (47068 kb)
cdf=Mouse430_2 (??? affyids)
Error: couldn't find function "exprs"
In addition: Warning message:
missing cdf environment ! in: show(list())
Error in ncol(exprs(x)) : Unable to find the argument "x" in selecting
a method for function "ncol"
## End of session.
I suspect that there must be something wrong with either the install or
that the calls used by affy became corrupt either at the source or
during the install. I should offer one caveat here. I have experienced
this problem with affy ever since I first installed it two weeks ago. I
have attempted to do re-installs of the affy package and clean installs
of R. Nothing has remedied this issue. And when I say clean install, I
mean I have crawled through the system and deleted everything from the
libraries to the install .pkg that OsX likes to hide. I also deleted
preferences. I also check system level and user level libraries to
ensure I got everything that was installed prior to the clean install.
If I try to do a reinstall over the current package I get the following
session:
trying URL `http://www.bioconductor.org/src/contrib/PACKAGES'
Content type `text/plain' length 46409 bytes
opened URL
==================================================
downloaded 45Kb
trying URL `http://www.bioconductor.org/src/contrib/PACKAGES'
Content type `text/plain' length 46409 bytes
opened URL
==================================================
downloaded 45Kb
trying URL `http://www.bioconductor.org/src/contrib/affy_1.5.8.tar.gz'
Content type `application/x-tar' length 1076622 bytes
opened URL
==================================================
downloaded 1051Kb
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... /lib/cpp
checking for main in -lz... no
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
/Library/Frameworks/R.framework/Resources/bin/SHLIB: line 1: make:
command not found
** Removing
'/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/affy'
** Restoring previous
'/Library/Frameworks/R.framework/Versions/2.0.1/Resources/library/affy'
ERROR: compilation failed for package 'affy'
>
Delete downloaded files (y/N)? y ##I deleted the file this
time, but have and haven't at other times.
>
It is at this point, I toss up my hands and beg for help. Sorry for the
length of this I wanted to be as thorough as possible could. I really
do appreciate the help.
Chad.
On Jan 25, 2005, at 1:57 PM, Robert Gentleman wrote:
>
> On Jan 25, 2005, at 9:35 AM, Chad Wayne wrote:
>
>> I appreciate you taking the time to answer my questions.
>>
>>>
>>> On Jan 24, 2005, at 12:55 PM, Chad Wayne wrote:
>>>
>>>> It was recommended that I post this problem to the mailing list. I
>>>> am unable to get affy to work, e.g. the library loads into R, but
>>>> the functions don't seem to work. I was hoping someone may have
>>>> seen this problem before and may have a solution. I am working in
>>>> the correct working directory.
>>>>
>>>> I am using version v2.0.1 of R with the default Bioconductor
>>>> package installed. Current package of Affy is 1.5.8. I am using Mac
>>>> OS X 10.3.7 and running X11 (X11 1.0 - XFree86 4.3.0). This is a
>>>> shared environment and all packages were installed in the top
>>>> library, not in the User library.
>>>>
>>>> On prompt:
>>>> > load("/nnn/nnn/nnn/timecourse.RData")
>>>
>>>> > library(affy)
>>>> Loading required package: Biobase
>>>> Loading required package: tools
>>>> Loading required package: reposTools
>>>
>>> So, if you go
>>> search()
>>> at this point you should get something like:
>>> > search()
>>> [1] ".GlobalEnv" "package:affy" "package:reposTools"
>>> [4] "package:Biobase" "package:tools" "package:methods"
>>> [7] "package:stats" "package:graphics" "package:grDevices"
>>> [10] "package:utils" "package:datasets" "Autoloads"
>>> [13] "package:base"
>>>
>>> The important things are for affy and Biobase to be there (at least
>>> given what you are saying below)
>>>
>>
>> I loaded affy and did the search as you suggested:
>>
>> > library(affy)
>> Loading required package: Biobase
>> Loading required package: tools
>> Loading required package: reposTools
>> > search()
>> [1] ".GlobalEnv" "package:affy" "package:reposTools"
>> [4] "package:Biobase" "package:tools" "package:methods"
>> [7] "package:stats" "package:graphics" "package:grDevices"
>> [10] "package:utils" "package:datasets" "Autoloads"
>> [13] "package:base"
>>
>> Appears to be there along with biobase.
>>
>>
>>>> > ReadAffy(widget=T)
>>>> Error: couldn't find function "ReadAffy"
>>>> > ReadAffy()
>>>> Error: couldn't find function "ReadAffy"
>>>> > pData(eset)
>>>> Error: couldn't find function "pData"
>>>>
>>>
>>>
>>> You can also try something like
>>> ls("package:affy")
>>>
>>> which should show about 116 things (mostly functions) and one should
>>> be ReadAffy.
>>>
>>
>> I also performed the ls("package:affy") and retrieved 116 items. I
>> attempted again to try the ReadAffy function and it failed.
>>
>
> Hmm, this seems really odd. So a whole bunch of questions in the
> hopes that one of them sheds some light on what your problem is.
> Basically, if the library is attached and the function is listed, it
> is there (or ought to be). Please show the entire transcript of you
> session (in answering the questions below, not just the part you want
> to) [possibly skipping to the end, as I now suspect that you do not
> have enough system software installed - we should think about how to
> find that out more automatically]
>
> If you just type ReadAffy, what happens?
> what if you type the name of one of the other functions (in any of the
> packages)?
> what is .libPaths() reporting?
>
>
>>> If not, then the installation is not correct. Are you sure they have
>>> global read permission etc on the R library directory and all
>>> contents? Have you checked to see if there are any files
>>> in those directories?
>>>
>>
>> Do I need to go to terminal to change the permissions or is there a
>> nice simple way to check permissions and change them accordingly if
>> that is the problem. Sorry that this appears so dense, but I haven't
>> quite got the hang of the unix side of OsX yet.
>>
>
> I doubt I was right about that; but there is nothing special going on
> on OS X, you do need a lot of stuff installed though - and that might
> be your problem.
>
> try this:
> > capabilities()
> jpeg png tcltk X11 http/ftp sockets libxml fifo
> TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> cledit IEEE754 iconv
> TRUE TRUE TRUE
>
> And in particular you are going to need X11 and tcltk (and you want
> most of the others). The R FAQ for OS X provides explicit details on
> how to do this.
>
> Robert
>
>
>> Thanks again,
>>
>> Chad.
>>
>>> Robert
>>>
>>>> I've also attempted to "start from scratch" from the original .cel
>>>> files and get the same type of error message that the function
>>>> couldn't be found.
>>>>
>>>> I have checked to ensure that affy is installed and loaded, and
>>>> based on the Package Manager, it is .
>>>>
>>>>
>>>> I've also tried using limma (v1.8.10), and had no problems, other
>>>> than I can't read in the eset.
>>>>
>>>> > packageDescription("limma", field="Version")
>>>> [1] "1.8.10"
>>>> > packageDescription("affy", field="Version")
>>>> [1] "1.5.8"
>>>> > version
>>>> _
>>>> platform powerpc-apple-darwin6.8
>>>> arch powerpc
>>>> os darwin6.8
>>>> system powerpc, darwin6.8
>>>> status
>>>> major 2
>>>> minor 0.1
>>>> year 2004
>>>> month 11
>>>> day 15
>>>> language R
>>>>
>>>>
>>>> Thanks for the assistance.
>>>>
>>>> Chad Wayne
>>>>
>>>> Chad M. Wayne, Ph. D.
>>>> Baylor College of Medicine
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>
>>>>
>>> +--------------------------------------------------------------------
>>> -------------------+
>>> | Robert Gentleman phone: (206) 667-7700
>>> |
>>> | Head, Program in Computational Biology fax: (206) 667-1319 |
>>> | Division of Public Health Sciences office: M2-B865
>>> |
>>> | Fred Hutchinson Cancer Research Center
>>> |
>>> | email: rgentlem at fhcrc.org
>>> |
>>> +--------------------------------------------------------------------
>>> -------------------+
>>>
>>>
>>
>>
> +----------------------------------------------------------------------
> -----------------+
> | Robert Gentleman phone: (206) 667-7700
> |
> | Head, Program in Computational Biology fax: (206) 667-1319 |
> | Division of Public Health Sciences office: M2-B865
> |
> | Fred Hutchinson Cancer Research Center
> |
> | email: rgentlem at fhcrc.org
> |
> +----------------------------------------------------------------------
> -----------------+
>
>
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