User: sanj

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sanj20
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New User
Location:
United Kingdom
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3 years, 1 month ago
Joined:
6 years, 6 months ago
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Posts by sanj

<prev • 9 results • page 1 of 1 • next >
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Block design for maSigPro
... Hi, I am using maSigPro for an NGS time series analysis on 10 different patients at 5 different time points T0,T1,T2,T3 and T4 (=50 samples in total). We introduce an insult after T0 and I want to do a trend analysis pre and post insult using masigpro across the time-points. I was wondering if it i ...
timecourse masigpro written 3.2 years ago by sanj20
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How to use brainarray custom cdf with oligo package?
... Hi, I have two datasets from HTA platform for which I want to do fRMA normalisation(specifically). As I understand fRMA works with either affybatch object(package affy) or ExpressionFeatureSet(package oligo). How can I do this by using custom cdf file from brain array resource? I have tried using t ...
customcdf oligo frma hta written 4.1 years ago by sanj20 • updated 4.1 years ago by James W. MacDonald51k
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Using maPredictDSC with Illumina bead chip
... Hi, Is it possible to use the maPredictDSC package on a dataset generated on Illumina HT-12 V3 bead chip? I know its compatible with the different affymetrix platforms but I am not sure how to use it with Illumina?  Thanks.       ...
mapredictdsc illumina beadchip written 4.5 years ago by sanj20
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Comment: C: UPC and Sequence file to remove GC bias
... Thanks for the reply. When I used the UPC detection function with the Affymetrix platform the function runs through the iterations but each time it shows No correction will be made for GC content. That confused me a bit but I think that is probably because no argument is passed to the sequenceFeatur ...
written 4.5 years ago by sanj20
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UPC and Sequence file to remove GC bias
... Hi,   I have been trying to use UPC_Generic_ExpressionSet function from the SCAN UPC package with Human Exon Array dataset and was stuck at a point. I want to use UPC based detection and correct for GC content but the sequence file for Affymetrix is at probe level whereas I am using alternative ex ...
upc_generic_expressionset brainarray written 4.5 years ago by sanj20 • updated 4.5 years ago by Stephen Piccolo560
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(Closed) UPC and Sequence file to remove GC bias
... Hi,   I have been trying to use UPC_Generic_ExpressionSet function from the SCAN UPC package with Human Exon Array dataset and was stuck at a point. I want to use UPC based detection and correct for GC content but the sequence file for Affymetrix is at probe level whereas I am using alternative ex ...
upc_generic_expressionset brainarray written 4.5 years ago by sanj20
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Answer: A: SCAN UPC normalisation
... Thanks for the reply. After the SCAN normalisation I have used the UPC detection method on around 4 different datasets, 3 of which are on affymetrix platform and 1 is on Illumina HT-12 V3 expression beadchip. The distribution of the detection value seems to be on extreme ends that is either 0 or 1 ...
written 4.5 years ago by sanj20
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SCAN UPC normalisation
... Hi,   I am using SCAN.UPC package to get batch effect adjusted intensities for two HGU133Plus2 datasets. However for few probesets I get negative intensity values. I understand that the data is log transformed but is there any way to avoid  that and get the intensities on a linear scale without an ...
normalization scan.upc written 4.6 years ago by sanj20
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Setting up design matrix in Limma
... Hi BioC users I am working with affymetrix exon array data of 40 samples with 8 different groups and 5 replicates of each. Two different strains are used in this study. Cells were cultured for either 3 days or 7 days. At 3 days the cells are still proliferating and are not considered mature , whe ...
sva written 6.5 years ago by sanj20

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to use brainarray custom cdf with oligo package?

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