Entering edit mode
Stephen Nyangoma
▴
230
@stephen-nyangoma-366
Last seen 9.7 years ago
Dear All,
I want to obtain expression values based on my data using Li-Wong
method. I gave the following command
liwongexpre<-expresso(Data2,normalize.method="invariantset",bg.correct
=FALSE,
pmcorrect.method="pmonly",summary.method="liwong")
It looks like I do not attain convergence. Is may call function ok?
> Data2
AffyBatch object
size of arrays=640x640 features (12803 kb)
cdf=MG_U74Av2 (12488 affyids)
number of samples=4
number of genes=12488
annotation=mgu74av2
>
Data2<-ReadAffy(filenames=c("../M7SS02080619.CEL","../M7SS02080607.CEL
")
> colnames(exprs(Data2))<- c("BXD5a","BXD9a")
>
liwongexpre<-expresso(Data2,normalize.method="invariantset",bg.correct
=FALSE,pmcorrect.method="pmonly",summary.method="liwong")
normalization: invariantset
PM/MM correction : pmonly
expression values: liwong
normalizing...done.
12488 ids to be processed
.........
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
2: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
3: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
4: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
5: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
6: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
7: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
8: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
9: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
10: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
11: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
12: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
13: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
14: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
15: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
16: No convergence achieved, too many outliers in: fit.li.wong(probes,
...)
