User: amin.ghareyazi

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Posts by amin.ghareyazi

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Comment: 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.ghareyazi0
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Comment: 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.ghareyazi0
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illumina ht 12 v4 data analysis
... 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 ...
illumina gene expression limma deg annotation written 18 months ago by amin.ghareyazi0 • updated 18 months ago by Gordon Smyth2.3k
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Comment: C: RNA-seq batch effect removal before DEseq2
... 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.ghareyazi0
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RNA-seq batch effect removal before DEseq2
... 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 ...
R rna-seq written 19 months ago by amin.ghareyazi0

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