User: pennakiza

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pennakiza40
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Posts by pennakiza

<prev • 26 results • page 1 of 3 • next >
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Comment: C: logFC in topTable problem- almost identical to average expression
... Thanks Kevin, I ran it again from scratch, it seems now that my results are not significant, since the toptable is empty. Thanks for all you help! ...
written 8 days ago by pennakiza40
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Comment: C: logFC in topTable problem- almost identical to average expression
... Oops, sorry, wrong data set! Here's the correct one, that's before the calcNormFactors: WTCHG_444413_209107 WTCHG_444413_225109 WTCHG_444413_214167 653635 334 270 406 102466751 9 7 7 ...
written 9 days ago by pennakiza40
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Comment: C: logFC in topTable problem- almost identical to average expression
... That's my contrasts matrix: Contrasts Levels EvsL LvsE Early 1 -1 Late -1 1 And that's my design matrix: Early Late 7 1 0 23 0 1 29 0 1 34 0 1 43 1 0 47 1 0 attr(,"assign") [1] 1 1 at ...
written 9 days ago by pennakiza40
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Comment: C: logFC in topTable problem- almost identical to average expression
... Yes, indeed it's very strange! These are the only too levels in my progression column! ...
written 9 days ago by pennakiza40
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Comment: C: logFC in topTable problem- almost identical to average expression
... Yeah, I can't say that they're massively high... for example: WTCHG_444413_216191 WTCHG_444413_217108 100287102 0 1 653635 140 244 102466751 0 6 100302278 ...
written 9 days ago by pennakiza40
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Comment: C: logFC in topTable problem- almost identical to average expression
... Hi Devon, This is how my df looks like: WTCHG_444413_209107 Early SJA023044 WTCHG_444413_225109 Late SJH027017 WTCHG_444413_214167 Late SJJ027008 WTCHG_444413_226121 Late SJK023006 WTCHG_444413_215179 Early SJR026007 WTCHG_444413_216191 Early ...
written 9 days ago by pennakiza40
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Comment: C: logFC in topTable problem- almost identical to average expression
... Thank you Kevin! Same results without the normalisation!! isexpr_df FALSE TRUE 13490 14905 And my MDS plot looks like that: (Red-Late, Green-Early) https://ibb.co/yy0nqF6 ...
written 10 days ago by pennakiza40
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Comment: C: logFC in topTable problem- almost identical to average expression
... Hi Kevin, Yes, I know, but not as fun as winning the lottery! :/ I've used feature counts and edgeR, as follows: fc_df <- featureCounts(files=filenames,annot.inbuilt="hg38",isPairedEnd = T) colnames(fc_df$counts)<-df$Sample y_df <- DGEList(counts = fc_df$counts, genes = ...
written 10 days ago by pennakiza40
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Comment: C: logFC in topTable problem- almost identical to average expression
... Hi Amar, I've tried it completely without contrasts too and the results are the same. Also, when I use a different contrast (or different coefficient in the case of no contrasts) the results look exactly the same! ...
written 10 days ago by pennakiza40
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logFC in topTable problem- almost identical to average expression
... Hi all, I am trying to analyze a dataset of samples that had early or late progression and I am using limma. My code is as follows: design<-model.matrix(~ 0 + df$progression, data = df) colnames(design)<- levels(df$progression) contr<-makeContrasts(EvsL=Early-Late, LvsE=Late- ...
R bioconductor limma rna-seq voom written 10 days ago by pennakiza40 • updated 9 days ago by russhh4.9k

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