User: Hao Liu

gravatar for Hao Liu
Hao Liu130
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13 years, 4 months ago
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15 years, 6 months ago
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l****@umdnj.edu

Posts by Hao Liu

<prev • 13 results • page 1 of 2 • next >
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R crashes on winXP with 2G memory
... Dear All: I encountered this several times, could someone point out where the problem is? I don't think it is the memory restriction or something... I have 345 MAS5 results formated as: probeset_id, expression_value, PA_call in 345 text file. I tried to combine them into one single file, but only ...
written 13.4 years ago by Hao Liu130
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Comment: C: matchprobes for GCRMA
... Dear All: I have a txt file with MAS5 read outs of 201 133A chips, I did it in windows. I have read it into R and I just wonder how do I make an exprset from it. (my MAS5 file only contains the signal intensity information, with probe_sets the leftest column, one sample per column across the whole ...
written 14.9 years ago by Hao Liu130
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Answer: A: RNA degradation plots
... Dear all: I read 12 cDNA experimental data into RGwt, when I use plotMA, only 1 shows up, how do I show others? I can't find documentation for it anywhere. Thanks Hao Liu, Ph. D ...
written 15.1 years ago by Hao Liu130
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Answer: A: How to put out the normalization result of limma as a *.txt file?
... Dear All: I wonder if there is a way to read in all the CEL file for a project using ReadAffy(), my Linux workstation has 2G memory but apparently it is not enough for 200 chips (HGU133). Anyway to bypass this? Or can I read them in separately, then combine them later? Thanks Hao ...
written 15.2 years ago by Hao Liu130
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how to match matrix
... I have a specific question in R to ask, in my phenodata, sometimes two chip results are from the same patient, one for primary cancer one for metastasis, I know I can do this to extract all chip results from a specific tissue: exprs(obj)[,which(pData(obj)[,2]=="liver")] I wonder if there is a way ...
cancer written 15.3 years ago by Hao Liu130
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Comment: C: tissue contamination problem in microarray
... hi! Wolfgang: I actually talked with some very good pathologists, according to them even microdissected sample (cancer tissue) could have around 20% contamination from surrounding tissue. Your answer to my question makes me wonder if I heard is true, can someone help to clarify this issue? Thanks ...
written 15.3 years ago by Hao Liu130
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tissue contamination problem in microarray
... Dear All: I would like to know if there are techniques to minimize the perturbation caused by tissue contamination, for example, normal lung tissue contamination on a breast metastasis. What is the best strategy to deal with this problem? I think this should be dealt with at the "low" level normal ...
breast lung written 15.3 years ago by Hao Liu130 • updated 15.3 years ago by Oosting, J. PATH550
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getting MAS for a large affy object
... Dear All: I read 178 affy results into on object using ReadAffy(). however, when I tried to computer MAS, the computer apparently don't have enough memory to complete the operation. I wonder if there is anyway to circumvent this. Another question is after getting MAS, how do I write results to di ...
affy written 15.3 years ago by Hao Liu130 • updated 15.3 years ago by James W. MacDonald50k
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newbie question: how do I get affy annotations
... Dear All: can someone teach me how to get affy libraries into R? I just tried library(hu6800) and I doubt if there are any other libraries there. Best regards Hao Liu, Ph. D ...
affy written 15.5 years ago by Hao Liu130 • updated 15.5 years ago by John Zhang2.9k
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Comment: C: get exprs from AffyBatch
... I got this message using mas5: mascolon <- mas5(myAffyBatch,normalize=TRUE, sc=150, analysis="ablolute"); background correction: mas PM/MM correction : mas expression values: mas background correcting...Error: cannot allocate vector of size 585042 Kb My AffyBatch has 151 samples, could this be ...
written 15.6 years ago by Hao Liu130

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Popular Question 13.4 years ago, created a question with more than 1,000 views. For how do I add pheno data after making AffyBatch object

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