User: pennakiza

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pennakiza60
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Posts by pennakiza

<prev • 37 results • page 2 of 4 • next >
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Decontaminate RNASeq data from other cell types?
... Hello all, Very ambitious question coming! So I have RNA Seq data from CD4+ cells, which are selected using a kit. However I used CIBERSORT on them and I see that there is a significant contamination with other immune cell types, mainly B and NK cells. I was wondering if there is any way to extract ...
gene expression rna seq decontamination written 14 months ago by pennakiza60
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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 15 months ago by pennakiza60
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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 15 months ago by pennakiza60
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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 15 months ago by pennakiza60
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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 15 months ago by pennakiza60
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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 15 months ago by pennakiza60
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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 15 months ago by pennakiza60
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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 15 months ago by pennakiza60
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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 15 months ago by pennakiza60
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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 15 months ago by pennakiza60

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Popular Question 19 days ago, created a question with more than 1,000 views. For DESeq2 object problem with padj
Popular Question 2.1 years ago, created a question with more than 1,000 views. For DESeq2 object problem with padj

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