Hi Libing.
I'm afraid that aroma.affymetrix will not work on TXT files. I
suggest you check out the following functions in the 'affxparser'
package:
?readCel (just so you know what is stored)
?createCel (to create the file)
?updateCel (to store intensities in the file)
Once you figure out
Hi Mark,
Thanks for your help so far! Now I have a quick question for you. Is there
any ways to get the probe ID for background corrected probe intensities? If
I have finish the following steps:
bc - RmaBackgroundCorrection(cs, tag=core,A20071112,EP)
csBC - process(bc, verbose=verbose)
Thanks!
Hi Hailei.
This has been discussed before as well. You might start with:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/36d8c59d742fc503/
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/f4d015cae1848f51/
You should definitely take log2 before
Hi Libing.
Doesn't 'addNames=TRUE' already do this for you?
fs1 - extractDataFrame(fs, units=1:2, addNames=TRUE)
head(fs1[,1:6])
unitName groupName unit group cell huex_wta_breast_A
1 2315251 23152521 11 1.1150999
2 2315251 23152531 22
Thanks! Mark:
I assume that you referred me to the probeset annotation csv file ,
not the transcript annotation csv file. :)
I did get the exon coordinates! it seemed to me that the probeset_id
in the probeset annotation file is equivalent to groupName of
exFirma.
One question I have is in the
I assume that you referred me to the probeset annotation csv file ,
not the transcript annotation csv file. :)
I did get the exon coordinates! it seemed to me that the probeset_id
in the probeset annotation file is equivalent to groupName of
exFirma.
Yes! The transcript CSV file may be
Hi, Mark:
Thanks again, here comes more questions :)
I got the example from one of the threads here, the original post was:
library(limma)
fit-lmFit(exFirma[,6:ncol(exFirma)], model.matrix(~
your.class.variable))
fit-eBayes(fit)
I thought I should be ok to define the design , then fit to it.
Ok, I just used the following line to read Affy Annotation
read.csv(file=MoEx-1_0-st-
v1.na27.mm9.transcript.csv,head=TRUE,sep=,,skip=20)
then I used
match(exFirma[x2$ID,1],affyAnnotation$transcript_cluster_Id)
but I only got NAs
I can not figure out what went wrong because I checked the
Hi Sabrina.
Indeed, you'll want to set 'mergeGroups=TRUE' for the probe level
model (ExonRmaPlm object) that you send to 'FirmaModel' ...
-
http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis
says:
...
plmTr - ExonRmaPlm(csN, mergeGroups=TRUE)
print(plmTr)
