User: tasnif.rahman

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Posts by tasnif.rahman

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Comment: C: Question: Pair-wise DESeq Analysis with 3 Factor Levels - RNA-Seq
... I understand. How should I set up the single design for C vs A and B vs A? Can I have more than one contrast comparison in one command? Also, I only used "design = ~ Chirality" to generate the dds, should that be okay with such comparisons? Thank you again, really appreciate the help.    ...
written 8 weeks ago by tasnif.rahman0
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Comment: C: Question: Pair-wise DESeq Analysis with 3 Factor Levels - RNA-Seq
... Yeah, they are basically different treatment conditions that pluripotent stem cells are treated with, and each condition leads to a CW or CWW bias. The stem cells themselves have no bias. I would like to compare the gene expression of groups with CW bias to the group with no bias. Do you reckon I sh ...
written 8 weeks ago by tasnif.rahman0
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Comment: C: Question: Pair-wise DESeq Analysis with 3 Factor Levels - RNA-Seq
... Hi Michael, thank you for your response. I have included the full coldata object. > as.data.frame(coldata)     Chirality           Cell.Type S11        NB               RUES2 S12        NB               RUES2 S13        NB               RUES2 S22        CW D5 Cardiac Mesoderm S23        CW D5 Ca ...
written 9 weeks ago by tasnif.rahman0
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Question: Pair-wise DESeq Analysis with 3 Factor Levels - RNA-Seq
... [ Crossposted from Biostars: https://www.biostars.org/p/348420/#348421 ] Hello, very new to RNA-Sequencing, R and DESeq2 so the question might be too simple or repeated so I apologize in advance. I am working with 24 RNA-Sequencing samples, 8 conditions with 3 biological replicates for each. A par ...
rnaseq deseq2 design model multiple factor levels written 9 weeks ago by tasnif.rahman0 • updated 9 weeks ago by Michael Love21k
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Combining biological replicates from raw counts for use in differential gene expression/normalization (DESeq2 and edgeR)
... I am new to RNA-Seq, Linux and R. I have raw counts from single-end RNA-Seq data for 8 different treatment conditions, with 3 biological replicates for each. I used the featureCounts command on Rsubread and have the raw counts matrix for all 24 samples at the meta-feature(gene) level. I was wonderin ...
differential gene expression biologicalreplicates raw_counts written 4 months ago by tasnif.rahman0 • updated 4 months ago by James W. MacDonald48k
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Comment: C: Trouble Installing Bioconductor Basic Packages
... That worked. Thank you!  ...
written 5 months ago by tasnif.rahman0
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Trouble Installing Bioconductor Basic Packages
... I am using R version 3.4.4 and Bioconductor version 3.6 with BiocInstaller version 1.28.0 on a Virtual Machine with Windows 7 as the host OS and Linux Mint 19 as the guest OS using VirtualBox version 4.3.12. When I try to install the basic BioConductor Packages with biocLite(), the packages do not i ...
bioclite R linuxmint installation problem virtualbox written 5 months ago by tasnif.rahman0 • updated 5 months ago by James W. MacDonald48k

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