User: sanj
sanj • 20
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- 20
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- New User
- Location:
- United Kingdom
- Last seen:
- 2 years, 11 months ago
- Joined:
- 6 years, 4 months ago
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Posts by sanj
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... 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 ...
written 3.0 years ago by
sanj • 20
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... 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 ...
written 3.9 years ago by
sanj • 20
• updated
3.9 years ago by
James W. MacDonald ♦ 50k
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... 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.
...
written 4.3 years ago by
sanj • 20
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... 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 4.4 years ago by
sanj • 20
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... 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 ...
written 4.4 years ago by
sanj • 20
• updated
4.4 years ago by
Stephen Piccolo • 560
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... 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 ...
written 4.4 years ago by
sanj • 20
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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 4.4 years ago by
sanj • 20
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... 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 ...
written 4.4 years ago by
sanj • 20
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... 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 ...
written 6.4 years ago by
sanj • 20
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