User: ying chen
ying chen • 340
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Posts by ying chen
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Comment:
C: affy( ) error with mas5()
... Hi guys,
Thanks a lot for the help and sorry for getting back to you so late
:(.
Now I got confused. Does it mean affy() cannot do a MAS5 of 3869 HG-
U133_Plus_2 arrays with affy CDF because of the setting of R long
vectors, or I did something wrong? I did a RMA with no problem.
Thanks,
Ying
&g ...
written 5.6 years ago by
ying chen • 340
0
votes
1
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1
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Comment:
C: countOverlaps Warnings
... Hi Martin,
Thanks a lot for the help! I believe it's due to some virus on my
computer as I just found out that my computer's antivirus programs all
got turned off and could not be turned back on. I am re-installing
Windows now and will try to re-install R and googleVis later.
Thanks,
Ying
> D ...
written 5.6 years ago by
ying chen • 340
0
votes
1
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914
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1
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Comment:
C: countOverlaps Warnings
... Hi guys,
I have this weird error when I tried to install googleVis package. I
installed it in my other PC with no problem and both runs Win7
Enterprise 64x. I tired to install from biocLite("googleVis"),
install.packages("googleVis"), install.packages() from downloaded
source, and had the same erro ...
written 5.6 years ago by
ying chen • 340
0
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2
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722
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... Hi Matt,
I just wonder is it possible for you to update the hgu133plus2frmavecs
packages to use the most recent customCDF v18?
Thanks a lot,
Ying
> Date: Tue, 22 Apr 2014 10:40:33 -0400
> From: mccallm@gmail.com
> To: sbrohee@ulb.ac.be
> CC: basvgestel@hotmail.com; bioconductor@r-pro ...
written 5.6 years ago by
ying chen • 340
0
votes
6
answers
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6
answers
... Hi guys,
I tried to draw plots similar to cbioportal's oncoprint plot, but have
no success yet. Here is an example of the oncoprint plot:
http://www.cbioportal.org/public-portal/index.do?cancer_study_id=luad_
tcga&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=luad_tcga_mutations
&genetic_pro ...
written 5.8 years ago by
ying chen • 340
0
votes
2
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1.2k
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2
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Answer:
A: Gviz: axes related parameters
... Hi guys,
I encounter this kind question quite a few times now and never have a
good answer. Say we have the expression data (microarray or RNAseq) of
gene A for both tumor and normal samples. The task is to detect how
many tumor samples have gene A over-expressed. I had tried to use
mean+2*stdev of ...
written 5.8 years ago by
ying chen • 340
0
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2
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1.8k
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2
answers
Answer:
A: EdgeR norm.factors input
... Hi guys,
I just got this weird error with CNTools package. Basically I tried to
map TCGA SNP6 level3 segmentation data to gene level. I have TCGA SNP6
level3 segmentation data fpor more than 16000 samples. All processed
well except for a block of 300 samples, which gave me the following
error messag ...
written 5.8 years ago by
ying chen • 340
0
votes
1
answer
617
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1
answers
... Hi guys,
I tried to install affxparser in R3.0.1 in Cygwin x64, but got some
errors.
Makevars:4: recipe for target
`fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o' failed
make: *** [fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o] Error
1
ERROR: compilation failed for package affxparse ...
written 6.2 years ago by
ying chen • 340
0
votes
1
answer
962
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1
answers
... Hi guys, I tried a sample with Variant Annotation's eadVcf. I ran the
code successfully in Linux (OK I had some warnings regarding "
unpackVcf field '..': NAs introduced by coercion"). But when I tried
the same code in R3.0.0 in windows 7, I got the error message: > for(i
in 1:length(vcflist1)){
...
written 6.6 years ago by
ying chen • 340
0
votes
1
answer
1.1k
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1
answer
... Hi guys, sorry to bother you again.
I am new to VariantAnnotation package and keep having some weird
errors when testing with TCGA vcfs.
> start.loc <- 55086725
> end.loc <- 55275031
> test.gr <- GRanges("7", IRanges(start.loc, end.loc))
> file <- system.file("vcf", "NA0698 ...
written 6.7 years ago by
ying chen • 340
• updated
6.7 years ago by
Martin Morgan ♦♦ 24k
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