User: amin.ghareyazi
amin.ghareyazi • 0
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Posts by amin.ghareyazi
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C: illumina ht 12 v4 data analysis
... And how should I use this annotation file? how can I pass it to limma with my data? ...
written 18 months ago by
amin.ghareyazi • 0
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C: illumina ht 12 v4 data analysis
... thanks Gordon. but what if some of the probes I have are control probes?
also I couldn't find any example for limma working without annotations. all I can find are examples that passes objects with annotations. can you give me at least a link to show me how it works? ...
written 18 months ago by
amin.ghareyazi • 0
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... Hi
I have a matrix of normalized microarray gene expression. probe-IDs are in rows and samples are in columns. I don't have any annotation files to pass to limma in order to start my analysis. I only know it is from illumina ht 12 v4 chip. Accession code refers to a GEO data that only covers a smal ...
written 18 months ago by
amin.ghareyazi • 0
• updated
18 months ago by
Gordon Smyth • 2.3k
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... thanks Kevin, it made a bit clear. My third question is a critical problem for me. can you help me on that? do you any method or pipeline like: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617154/][1]
[1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617154/ ...
written 19 months ago by
amin.ghareyazi • 0
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... Hi
I'm trying to analyze RNA-seq data of multiple ICGC projects. I want to remove batch effects of projects with SVA package and algorithm before employing DEseq2 for finding differentially expressed genes and after that network analysis. I have these questions:
1) DEseq2 uses only raw read counts ...
written 19 months ago by
amin.ghareyazi • 0
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