User: jeremy wilson

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jeremy wilson150
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Posts by jeremy wilson

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Comment: C: ArrayQualityMetrics: Grey boxes in boxplot
... Dear Audrey, thanks for your reply. The package is version 2.6 on R2.11. No, the asterisks are not displayed in the html report even though they are recognised as different from the rest by the package! I have attached the outlier summary section screemshot for your reference. Here is the sessionIn ...
written 9.0 years ago by jeremy wilson150
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ArrayQualityMetrics: Grey boxes in boxplot
... Dear all, I am noticing that some of my boxes in the boxplot are colored grey. I looked at the code to plot the boxplots (aqm.boxplot) and observed that there is a parameter "outlier" whose length if not zero will color the respective arrays as grey. These outliers as I understand from the code are ...
normalization written 9.0 years ago by jeremy wilson150 • updated 9.0 years ago by Audrey Kauffmann110
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Interpretation of genotype calls from Oligo crlmm algorithm
... Dear Bioconductors, I have genotyped 8 samples from Affy6.0 platform using crlmm algorithm from Oligo and I am facing difficulties in interpretation. I am trying to match the gender from the phenodata with the SNP calls from crlmm on X and Y chromosomes. I would appreciate any comments and help. Gi ...
snp oligo crlmm written 9.4 years ago by jeremy wilson150 • updated 9.4 years ago by Benilton Carvalho4.3k
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Comment: C: QC Affy 6.0 SNP arrays with crlmm or Oligo?
... Dear Benilton and Henrik, thanks for your suggestions. I read those papers you suggested and am planning to use CRLMM for the genotyping and the aroma.affy package for copy number analysis. Henrik, my data is not a paired sample data. I would need to get a robust average of the 8 samples for the nor ...
written 9.4 years ago by jeremy wilson150
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Comment: C: QC Affy 6.0 SNP arrays with crlmm or Oligo?
... Thanks for the reply dear Benilton.. how can then one proceed with QC'ing SNP arrays using BioC? Considering the quality of arrays are good, does the crlmm algorithm give good call rates with higher accuracy compared to the Birdseed algorithm from Affy genome console and the BirdSuit from Broad MI ...
written 9.4 years ago by jeremy wilson150
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QC Affy 6.0 SNP arrays with crlmm or Oligo?
... Dear all, I am wondering if there is a QC methodology like the "contrast QC" check by the affymetrix genome console to QC the arrays before genotyping. The crlmm and Oligo packages do the normalization and summarization which is awesome but I do not see it doing QC checks. I am trying to see the qu ...
normalization oligo crlmm written 9.4 years ago by jeremy wilson150 • updated 9.4 years ago by Benilton Carvalho4.3k
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Comment: C: HTqPCR: Calculate CV between replicates with in a plate
... Thanks for your reply Dr.Heidi, the input files are from ABI RQ analysis (tab delimited text files). I can directly read these files using the readCtData function. I see discussions about not able to read files from RQ analysis output if the text file is a compilation of more than 1 sample. I have ...
written 9.5 years ago by jeremy wilson150
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HTqPCR: Calculate CV between replicates with in a plate
... Dear list, I see that the package considers each plate as different sample and calculates CV for genes across plates (samples) but not with in a plate. Unfortunately my plate design is different. I have 384 well plates with 3 replicates for 32 genes in first 4 rows of the plate. Likewise other 3 s ...
written 9.5 years ago by jeremy wilson150 • updated 9.5 years ago by Heidi Dvinge2.0k
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background correcting an eset from GEO query
... Dear BioConductors, I am using GEO query to get valuable datasets from GEO database for my analysis. Most of the datasets I require have not submitted raw data and I have to rely on the SOFT files to get the expression set directly using the "getGEO" command. When I plot the intensities of the expr ...
normalization written 9.6 years ago by jeremy wilson150 • updated 9.6 years ago by Sean Davis21k
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Answer: A: Fwd: maSigPro - NA values for coefficient estimates - Is a polynomical fit recom
... Dear Ana, thanks a lot for the very helpful suggestions. You guided me in the right direction. The analysis makes exact sense of my data. On Tue, Nov 10, 2009 at 7:20 AM, Ana Conesa wrote: > Dear Jeremy > > My apologies for the late response. > First of all: maSigPro compares profile ...
written 9.8 years ago by jeremy wilson150

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