Re: Could not locate a file for this chip type (Was: Re: [aroma.affymetrix] aroma.affymetrix)

[Henrik Bengtsson]

Hi.

On Wed, Aug 26, 2009 at 12:10 PM, Diya Vaka<biote...@gmail.com> wrote:
>
> Hi all,
>
> I am trying to analyze MoGene-1_0-st-v1 data and I these are the
> errors:
>
> In MoGene-1_0-st-v1 directory I have the MoGene-1_0-st-v1.cdf file and
> I ran the following commands
>
> setwd("C:/Documents and Settings/annotationData/chipTypes/MoGene-1_0-
> st-v1/")
>> getwd()
> [1] "C:/Documents and Settings/annotationData/chipTypes/MoGene-1_0-st-
> v1"
>> chipType <- "MoGene-1_0-st-v1"
>> cdf <- AffymetrixCdfFile$fromChipType(chipType)

Not the cause of the problem, but please use byChipType() not
fromChipType() - who told you to use fromChipType()?

> Error in list(`AffymetrixCdfFile$fromChipType(chipType)` =
> <environment>,  :
>
> [2009-08-26 13:25:55] Exception: Could not locate a file for this chip
> type: MoGene-1_0-st-v1
>  at throw(Exception(...))
>  at throw.default("Could not locate a file for this chip type: ",
> paste(c(chipT
>  at throw("Could not locate a file for this chip type: ", paste(c
> (chipType, tag
>  at byChipType.UnitNamesFile(static, ...)
>  at byChipType(static, ...)
>  at method(static, ...)
>  at AffymetrixCdfFile$fromChipType(chipType)

It is correct that annotation files for the 'MoGene-1_0-st-v1' chip
type should be located in a directory

annotationData/chipTypes/MoGene-1_0-st-v1/

but it is also important to understand that this is the path
aroma.affymetrix uses to look up those files, that is, your working
directory should not be that directory but, in your case, C:/Documents
and Settings/.

Here is a troubleshooting script:

library("aroma.affymetrix")
stopifnot(isDirectory("annotationData"))
stopifnot(isDirectory("annotationData/chipTypes"))
stopifnot(isDirectory("annotationData/chipTypes/MoGene-1_0-st-v1/"))
stopifnot(isFile("annotationData/chipTypes/MoGene-1_0-st-v1/MoGene-1_0-st-v1.cdf"))

(the above won't work if you use Windows Shortcut links, but I don't you do).

You can read more on Page 'Setting up annotation files':

http://groups.google.com/group/aroma-affymetrix/web/setup

Hope this helps

Henrik

>
> Can anyone help me
>
> Thanks
>
> Diya
>
> >
>

[Diya Vaka]

Dear Henrik,

Thank you for the help.Now its running fine.

I want to get the top 100 over expressed genes and under expressed
genes from this data.

So can I use the affy and limma packages for that or is there any
thing specifically in aroma.affymetrix.

Thanks in advance,

Diya

[Henrik Bengtsson]

On Thu, Aug 27, 2009 at 10:12 AM, Diya Vaka<biote...@gmail.com> wrote:
>
> Dear Henrik,
>
> Thank you for the help.Now its running fine.

Good.

>
> I want to get the top 100 over expressed genes and under expressed
> genes from this data.
>
> So can I use the affy and limma packages for that or is there any
> thing specifically in aroma.affymetrix.

Please start a new thread with a descriptive subject line (and as
detailed question as possible) whenever the question changes. This
new question has nothing to do with "Could not locate a file for this
chip type"). Your previous message was titled "aroma.affymetrix"
(which I changed); go to
http://groups.google.com/group/aroma-affymetrix/topics - imagine if
all people would write "aroma.affymetrix" in the subject line. So,
please spend some time on the subject line.

I consider this new question to be answered in thread
'"gene-1-0-st-array-analysis" - Discussion' started on Aug 27, 2007 [
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/9ee424979095c462
].

Cheers,

/Henrik

[Mathieu Parent]

I just answered this question at:

http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array-analysis

regards,
Math
McGill Uni

[JeromeW]

Hi all

I reply in this thread because I also have the "could not locate a
file" problem which I cannot solve.

My code:
setwd("/x05/people/m140932/eclipse/workspace/CNV"); # here I set the
working directory
library("aroma.affymetrix");
log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
options(digits=4);

stopifnot(isDirectory("annotationData"));
stopifnot(isDirectory("annotationData/chipTypes"));

stopifnot(isDirectory("annotationData/chipTypes/GenomeWideSNP_6"));
stopifnot(isFile("annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf"));
cdf <- AffymetrixCdfFile$byChipType("GemomeWideSNP_6", tags="Full");

My paths and files:
>pwd
/x05/people/m140932/eclipse/workspace/CNV/annotationData/chipTypes/
GenomeWideSNP_6
>ll
total 673949
-rw-r--r-- 1 scicomp 493291745 2009-09-01 16:49
GenomeWideSNP_6,Full.cdf
-rw-r--r-- 1 scicomp 7526454 2009-09-02 07:54
GenomeWideSNP_6,Full,na26,HB20080722.ufl
-rw-r--r-- 1 scicomp 9407937 2009-09-02 07:55
GenomeWideSNP_6,Full,na26,HB20080821.ugp
-rw-r--r-- 1 scicomp 179217531 2009-09-02 08:03
GenomeWideSNP_6,HB20080710.acs

I checked many times the paths and filenames but cannot see the error.
I still get the following error message:
Error in list(`AffymetrixCdfFile$byChipType("GemomeWideSNP_6", tags =
"Full")` = <environment>, :
[2009-09-02 09:09:17] Exception: Could not locate a file for this chip
type: GemomeWideSNP_6,Full

at throw(Exception(...))
at throw.default("Could not locate a file for this chip type: ",
paste(c(chipT
at throw("Could not locate a file for this chip type: ", paste(c
(chipType, tag

at method(static, ...)
at AffymetrixCdfFile$byChipType("GemomeWideSNP_6", tags = "Full")

I am using R2.9.1 on Linux (with the Eclipse StatET plug-in).

Thanks for your help
cheers
Jerome

[JeromeW]

(sorry for quoting myself)>

I am more and more puzzled... The "findByChipType" method seems to
correctly detect the cdf file:

AffymetrixCdfFile$findByChipType("GenomeWideSNP_6", tags="Full")
[1] "annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf"

[Henrik Bengtsson]

So, if none of the stopifnot() tests complaints, then it might be that
the CDF file might be corrupt or incomplete. Compare with the file
size and checksum that I get:

> library("aroma.affymetrix");
> pathname <- "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
> df <- GenericDataFile(pathname);
> df
GenericDataFile:
Name: GenomeWideSNP_6
Tags: Full
Full name: GenomeWideSNP_6,Full
Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf
File size: 470.44 MB (493291745 bytes)
RAM: 0.00 MB
> getChecksum(df)
[1] "3fbe0f6e7c8a346105238a3f3d10d4ec"

/Henrik

[JeromeW]

Thank you Henrik for your quick reply.

Here is what I get:

> df <- GenericDataFile("annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf");

> df;
GenericDataFile:
Name: GenomeWideSNP_6
Tags: Full
Full name: GenomeWideSNP_6,Full
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf
File size: 470.44 MB (493291745 bytes)
RAM: 0.00 MB
> getChecksum(df)
[1] "3fbe0f6e7c8a346105238a3f3d10d4ec"

We have exactly the same file...

Cheers
Jerome

[Henrik Bengtsson]

Ok, next test:

> library("aroma.affymetrix");
> pathname <- "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";

> cdf <- AffymetrixCdfFile(pathname);
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4

Does this work for you?

/Henrik

>
> Cheers
> Jerome
> >
>

[Diya Vaka]

Hi,

I have created a cdf and I am trying to check how its running and I have have this error.Could anyone help me on this.

This is the code:
>  df<-GenericDataFile("annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf")
> chipType<-"HG-U133_Plus_2"
> cdf<-AffymetrixCdfFile$findByChipType(chipType)
> cdf
[1] "annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf"
> cdf<-AffymetrixCdfFile$byChipType(chipType)
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HG-U133_Plus_2
Filename: HG-U133_Plus_2.cdf
Filesize: 9.62MB
Chip type: HG-U133_Plus_2

RAM: 0.00MB
File format: v4 (binary; XDA)

Dimension: 1164x1164
Number of cells: 1354896
Number of units: 30604
Cells per unit: 44.27
Number of QC units: 0
> cs <- AffymetrixCelSet$fromName("parekh", cdf=cdf)
Error in list(`AffymetrixCelSet$fromName("parekh", cdf = cdf)` = <environment>,  :
  [2009-09-02 12:30:34] Exception: Cannot create AffymetrixCelSet.  No such directory: parekh/HG-U133_Plus_2
  at throw(Exception(...))
  at throw.default("Cannot create ", class(static)[1], ".  No such directory: ", path)
  at throw("Cannot create ", class(static)[1], ".  No such directory: ", path)
  at byName.AffymetrixCelSet(static, ...)
  at byName(static, ...)
  at method(static, ...)
  at AffymetrixCelSet$fromName("parekh", cdf = cdf)


Thanks,

Diya

[JeromeW]

> > library("aroma.affymetrix");
> > pathname <- "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
> > cdf <- AffymetrixCdfFile(pathname);

This works!
Thank you Henrik.

[Henrik Bengtsson]

No, no, that is supposed to be a a workaround - it is only for
troubleshooting! You should never ever have to specify paths in your
scripts, so don't consider the above as an option.

So, the CDF is located in the correct place. Continuing:

pathname <- "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
cdf <- AffymetrixCdfFile(pathname);

pathname <- getPathname(cdf);
print(pathname);

pathname2 <- AffymetrixCdfFile$findByChipType("GenomeWideSNP_6", tags="Full");
print(pathname2);

# The two pathnames should be the same
stopifnot(identical(pathname2, pathname));

If they are, then this *should* work:

cdf2 <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
print(cdf2);

Does it? If not, what does this give:

path <- getPath(cdf);
cat(list.files(path=path), sep="\n");

/Henrik


> >
>