Hi Yiwen.
Indeed, aroma.affymetrix supports custom CDF files.
For example (Human Exon 1.0 ST array with the Brainarray RefSeq custom
CDF):
http://groups.google.com/group/aroma-affymetrix/web/hsex10stv2-hs-refseq
As another example, say you were interested in the Human Gene 1.0 ST
array and
Hi,
I was wondering whether aroma-affymetrix package supports the use of custom
CDF.
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp
If yes, should I use the custom CDF the same way as CDF from Affy.
In addition, if I want to use RMA method to do backg
google.com/group/aroma-affymetrix/web/code-snippets
>> :
>> I've got an error at the summarization step:
>>
>>> plm <- RmaCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
>>> fit(plm, verbose=log)
>>
>> 20090806 12:42:04| Â Identifying non-fitted units i
Hi Anbarasu.
No, you don't have to remove all the files. What you can do is use
extract() to extract the files that you are interested in, and create
a new AffymetrixCelSet and fit the probe level modesl only on those
samples. You do need to be careful though and I suggest you use
*tags
analyzing a set of 250K SNP arrays using the CRMAv2
> code from http://groups.google.com/group/aroma-affymetrix/web/code-snippets
> :
> I've got an error at the summarization step:
>
>> plm <- RmaCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
>> fit(plm, verbose=log)
&
Hi,
I'm having trouble analyzing a set of 250K SNP arrays using the CRMAv2
code from http://groups.google.com/group/aroma-affymetrix/web/code-snippets:
I've got an error at the summarization step:
> plm <- RmaCnPlm(csN, mergeStrands=TRUE, combineAlleles=TRUE)
> fit(plm, ver
