[aroma.affymetrix] Error while setting up AffymetrixCelSet

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

[aroma.affymetrix] Error while setting up AffymetrixCelSet

Marijke VAN MOERBEKE-2
Dear all

I run into an error while setting up a CELset with my data. I've checked the structure of the folder annotationData and rawData and this is as instructed. My working directory contains the folders annotationData and rawData which both have a folder "hjay" (my chiptype) containing the cdf and CEL files respectively.  My code is as follows:

library(aroma.affymetrix)

chipType<-"hjay"
cdf <- AffymetrixCdfFile$byChipType(chipType,tags="r1,TC")
print(cdf)
# AffymetrixCdfFile:
# Path: annotationData/chipTypes/hjay
# Filename: hjay,r1,TC.cdf
# File size: 103.36 MiB (108385660 bytes)
# Chip type: hjay,r1,TC
# RAM: 0.00MB
# File format: v4 (binary; XDA)
# Dimension: 2558x2560
# Number of cells: 6548480
# Number of units: 33516
# Cells per unit: 195.38
# Number of QC units: 0

cs <- AffymetrixCelSet$byName("Data_Study1",cdf=cdf,verbose=TRUE);
#which runs into the following error

Exception: Failed to setup a data set for any of 1 data directories located. The following reasons were reported: (1) Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'hjay' (without requiring any tags) and with filename extension 'cdf'. (while trying './rawData/Data_Study1/hjay').

  at #03. byName.AffymetrixCelSet(static, ...)
          - byName.AffymetrixCelSet() is in environment 'aroma.affymetrix'

  at #02. byName(static, ...)
          - byName() is in environment 'R.filesets'
          - originating from '<text>'

  at #01. AffymetrixCelSet$byName("HTA_RASA", cdf = cdf, verbose = TRUE)
          - AffymetrixCelSet$byName() is local of the calling function

Error: Failed to setup a data set for any of 1 data directories located. The following reasons were reported: (1) Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'hjay' (without requiring any tags) and with filename extension 'cdf'. (while trying './rawData/HTA_RASA/hjay').

I created the cdf file myself. Is it possible that that I made a mistake during this process that can already be detected by AffymetrixCelSet$byName?

Thank you for any help!


--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
 
 
You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/

---
You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.
Reply | Threaded
Open this post in threaded view
|

Re: [aroma.affymetrix] Error while setting up AffymetrixCelSet

Henrik Bengtsson-2
Hmm... this looks weird but as usual, there's probably a simple
explanation to it.  Yes, it could possibly be that the CDF is
incompatible with the CEL files, but in that case I'd expect an
informative error message explaining why.

In a fresh R session, what does the following output?

library("aroma.affymetrix")
cdf <- AffymetrixCdfFile$byChipType("hjay", tags="r1,TC")
cs <- AffymetrixCelSet$byName("Data_Study1", cdf=cdf, verbose=-100)

The output is quite long, but it'll help me/you troubleshoot.

Also, what's the output of sessionInfo() after the above?

/Henrik

On Mon, Aug 1, 2016 at 1:17 PM, Marijke VAN MOERBEKE
<[hidden email]> wrote:

> Dear all
>
> I run into an error while setting up a CELset with my data. I've checked the
> structure of the folder annotationData and rawData and this is as
> instructed. My working directory contains the folders annotationData and
> rawData which both have a folder "hjay" (my chiptype) containing the cdf and
> CEL files respectively.  My code is as follows:
>
> library(aroma.affymetrix)
>
> chipType<-"hjay"
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="r1,TC")
> print(cdf)
> # AffymetrixCdfFile:
> # Path: annotationData/chipTypes/hjay
> # Filename: hjay,r1,TC.cdf
> # File size: 103.36 MiB (108385660 bytes)
> # Chip type: hjay,r1,TC
> # RAM: 0.00MB
> # File format: v4 (binary; XDA)
> # Dimension: 2558x2560
> # Number of cells: 6548480
> # Number of units: 33516
> # Cells per unit: 195.38
> # Number of QC units: 0
>
> cs <- AffymetrixCelSet$byName("Data_Study1",cdf=cdf,verbose=TRUE);
> #which runs into the following error
>
> Exception: Failed to setup a data set for any of 1 data directories located.
> The following reasons were reported: (1) Failed to create AffymetrixCdfFile
> object. Could not locate an annotation data file for chip type 'hjay'
> (without requiring any tags) and with filename extension 'cdf'. (while
> trying './rawData/Data_Study1/hjay').
>
>   at #03. byName.AffymetrixCelSet(static, ...)
>           - byName.AffymetrixCelSet() is in environment 'aroma.affymetrix'
>
>   at #02. byName(static, ...)
>           - byName() is in environment 'R.filesets'
>           - originating from '<text>'
>
>   at #01. AffymetrixCelSet$byName("HTA_RASA", cdf = cdf, verbose = TRUE)
>           - AffymetrixCelSet$byName() is local of the calling function
>
> Error: Failed to setup a data set for any of 1 data directories located. The
> following reasons were reported: (1) Failed to create AffymetrixCdfFile
> object. Could not locate an annotation data file for chip type 'hjay'
> (without requiring any tags) and with filename extension 'cdf'. (while
> trying './rawData/HTA_RASA/hjay').
>
> I created the cdf file myself. Is it possible that that I made a mistake
> during this process that can already be detected by AffymetrixCelSet$byName?
>
> Thank you for any help!
>
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [hidden email].
> For more options, visit https://groups.google.com/d/optout.

--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/

---
You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
For more options, visit https://groups.google.com/d/optout.