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DESeq2 raw

updated 2.2 years ago by swbarnes2 ★ 1.4k • written 2.2 years ago by Hicham ▴ 10

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.gpr raw Agilent MicroarrayData import

updated 3.2 years ago by Gordon Smyth 52k • written 3.2 years ago by irina.st.louis4 • 0

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CEL RAW geoquery readaffy

updated 10.3 years ago by Sean Davis 21k • written 10.3 years ago by PyPer ▴ 20

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Answer: I am having issues with bowtie2_build by James W. MacDonald 67k

Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…

Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k

Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…

Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k

FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…

Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10

I see. Thank you ATpoint!

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0

Thanks James!

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Answer: Unable to install nloptr

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