User: rahel14350

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rahel1435010
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United States
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3 months ago
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2 years, 2 months ago
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r*********@gmail.com

Posts by rahel14350

<prev • 31 results • page 1 of 4 • next >
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Comment: C: bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype argument
... Dear https://support.bioconductor.org/u/2979/ and Dear https://support.bioconductor.org/u/7579/, Many thanks for your help. I did repeat the Funnorm with nPcs=2 and I did find the probe with NA value using: pval = fit2$p.value and fitcoef= fit2$coef Then I went back to the filtration step and remo ...
written 5 months ago by rahel1435010
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Comment: C: bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype argument
... Dear https://support.bioconductor.org/u/7579/, Many thanks for your help and explanation. I am actually walking slowly. I did read the paper you linked here before and also I went through details of minfi, RnBeads, Methylumi and so on to choose the fitted analysis and normalization methods for my d ...
written 5 months ago by rahel1435010
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Comment: C: bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype argument
... Dear https://support.bioconductor.org/u/7579/, I checked the mVals and there is no NA in the matrix and if the mVals are enormous in both direction, is there any solution in this case? BTW, I have done cpg.annotate with a name from my contMatrix and I get the same error ... myAnnotation <- cpg ...
written 5 months ago by rahel1435010
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Comment: C: bug in cpg.annotate() and DMR.plot: bad defaults for what and arraytype argument
... Dear https://support.bioconductor.org/u/7579/ I have the same error. While I have the updated package. Can you please help m? myAnnotation <- cpg.annotate(datatype="array", mVals, what="M", arraytype="450K", analysis.type="differential", design=design, contrasts = TRUE, cont.matrix = contMatrix ...
written 5 months ago by rahel1435010
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Comment: C: how to do noob+funnorm+bmiq normalization together in minfi or RnBeads?
... Dear https://support.bioconductor.org/u/2979/, Many thanks for prompt reply. I got the idea from this paper, as they showed it is working better on cancer data. It is also because I have a high heterogeneity and variation between my samples and I wanted to compare different normalization possibilit ...
written 5 months ago by rahel1435010
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how to do noob+funnorm+bmiq normalization together in minfi or RnBeads?
... Dear https://support.bioconductor.org/u/2979/, Can you please help me with this question on Biostar (https://www.biostars.org/p/245859/). I want to do noob+funnorm+bmiq normalization on cancer samples using minfi. Is this possible?  Many thanks in advance, Rahel ...
minfi rnbeads bmiq noob preprocessfunnorm written 5 months ago by rahel1435010 • updated 5 months ago by Kasper Daniel Hansen6.3k
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how to use Methylumi background correction (noob) in CHAMP
... Dear https://support.bioconductor.org/u/3561/, I want to use noob pre-processing in CHAMP, but when I start with methylumi package it is not possible to convert the pre-processed data to CHAMP (as you explained in the package). Is there any way to do background correction using noob in CHAMP direc ...
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Comment: C: GLM model on time course analysis and removing the outliers in Deseq2
... Many thanks for your explanation. I decided to do factor based analysis and check the output for each time point separately ... ...
written 8 months ago by rahel1435010
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Comment: C: GLM model on time course analysis and removing the outliers in Deseq2
... Dear Michael, Many thanks for your time and reply. I understood and I will try to find a statistician around to help me further with a linear design of changes across time. Then, If I want to continue with DeSeq2, I go for Time as a factor and this design: DESeqDataSetFromTximport(txi, colData=co ...
written 8 months ago by rahel1435010
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Comment: C: GLM model on time course analysis and removing the outliers in Deseq2
... Dear Gavin,  Many thanks for your reply and explanation. I know if I use time as factor is more flexible but it is not any more linear ...  ...
written 8 months ago by rahel1435010

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