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Comment: C: Why the result of pairwise comparison and Anova comparison of the same contrast
... Thanks for your reply! In fact I would like to test which Genes differentially Express in H9.kI vs wt and H9.ko vs wt samples, then select common up-down regulated genes between those comparisons. I would like to know can I use Anova or I should consider single comparison, then find common Genes ...
written 13 hours ago by star0
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Why the result of pairwise comparison and Anova comparison of the same contrast is different ?
... I have a group line with 2 treatments and one control and I did DE using EdgeR. My design matrix is as below and I run contrast for those samples using pairwise and anova test. Although their LigFC are the same for DE genes, their FDR are different. data Ensembl_ID Gene_name ...
edger written 1 day ago by star0 • updated 12 hours ago by Gordon Smyth37k
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ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
... I like to use ChIPqc packages, so I used output of Bowtie2 (after deduplicating using Picards) as `Bam` file and used `narrowPeak` file as output of MACS2, but I faced with below Error. sample = ChIPQCsample("align-path/undup_uniqu_SRR5339509_ENCSR890NXD_control_2.bam", peaks="peak path/GSM253 ...
chipqc qc chip-seq written 3 months ago by star0

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