[aroma.affymetrix] Changing the Aroma settings (RMA MedianPolish threshold ) in the latest version of the aroma.affymetrix

[sanjana]

Hi,

Our group is working with HTA platform and using  aroma.affymetrix  for the 
analysis. We intend to change the RMA median polish threshold in aroma 
settings. We are able to achieve this in version 2.13.1 but somehow not in 
version 2.13.2?

Has anyone else experienced  the same thing? Is it possible there is a bug 
in the 2.13.2 version?

Thanks,

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[aroma.affymetrix] using custom CDF file in aroma.affymetrix

[sanjana]

Hi,

I am using a Custom cdf file  *HTA-2_0,Transcript,binary.cdf* in aroma. 
affymetrix to analyse HTA-2_0 chip .  I am using the following commands to 
set up CDF and CEL files.

>chipType <- "HTA-2_0"
>cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Transcript,binary")
>print(cdf)

AffymetrixCdfFile:
Path: annotationData/chipTypes/HTA-2_0
Filename: HTA-2_0,Transcript,binary.cdf
File size: 7.55 MB (7921066 bytes)
Chip type: HTA-2_0,Transcript,binary
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 18490
Cells per unit: 354.44
Number of QC units: 0

>cs<-AffymetrixCelSet$byName("Krzy",cdf=cdf,verbose=verbose)

However I am unable to read the CEL files as it gives me the following 
error:

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 'HTA-2_0' 
(without requiring any tags) and with filename extension 'cdf'. (while 
trying './rawData/Krzy/HTA-2_0').

My directory structure is: 
annotationData< chipTypeshttp://www.aroma-project.org/.
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