User: jivarajivaraj

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Posts by jivarajivaraj

<prev • 16 results • page 1 of 2 • next >
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Different results with DESeq2 and EdgeR
... Hi, I have done differential expression on same date with both of DESeq2 and EdgeR but I am seeing contradict results For instance DCK6 shows positive 1 fold change by DESeq2 while -1 fold change by EdgeR. I really got confused which one is right? > head(DESeq2) baseMean log2FoldChan ...
edger deseq2 written 4 hours ago by jivarajivaraj0 • updated 4 hours ago by Gordon Smyth36k
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Comment: C: Nanostring analysis with limma
... Sorry, I have digital raw read counts of HTG EdgeSeq Oncology Biomarker Panel (OBP). Whatever I am googling I am not finding anybody used DESeq2, limma, voom or EdgeR for differenial expresseion in this assay. In this assay the expression levels of 2559 genes are assessed. Do you thinK I can use the ...
written 3 days ago by jivarajivaraj0
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Comment: C: Can I use DESeq2 for special assays
... Thanks a lot In my digital raw read counts I have both negative, positive probes and house keeping genes as below Probe Set ESOBP ESOBP Well A1 A10 A11 A12 A2 A3 A4 Total Counts 2966772 3675646 5654645 120022 1895274 2977577 3156411 NEG_CTRL_ANT1 18 1 0 2 0 37 23 NEG_CTRL ...
written 3 days ago by jivarajivaraj0
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Can I use DESeq2 for special assays
... Hi, I have digital raw read counts of HTG EdgeSeq Oncology Biomarker Panel (OBP). Whatever I am googling I am not finding anybody used DESeq2 for differenial expresseion in this assay. I have done Differential expression with DESeq2 though. In this assay the expression levels of 2559 genes are asse ...
deseq2 targeted sequencing written 3 days ago by jivarajivaraj0 • updated 3 days ago by Michael Love21k
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Comment: C: Correcting the batch effect in Edgeseq data
... Sorry, I have obtained this > resultsNames(dds) [1] "Intercept" "cell_type_NOF_vs_CAF" "co_cultured_YES_vs_NO" [4] "cell_typeNOF.co_culturedYES" By > mycols cell_type co_cultured G2 NOF NO G3 NOF YES ...
written 11 days ago by jivarajivaraj0
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Correcting the batch effect in Edgeseq data
... Hi, I have raw read counts of 57 patients ranked with Mandard score as TRG12 and TRG45. Mandard score : **A histological assessment of the response of oesophageal cancers to neoadjuvant treatment (cisplatin chemotherapy and radiotherapy in the original paper). The tumour regression grades were de ...
deseq2 batch edgeseq written 12 days ago by jivarajivaraj0 • updated 12 days ago by Michael Love21k
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Comment: C: Plotting several heatmaps onto the same grid with the ComplexHeatmap package in
... Sorry, when plotting two heatmaps with the genes with same ordering by complexheatmap, how i can put the same color scaling on the both heat maps? because one of my heat maps is darker in genes blocks =https://image.ibb.co/fbhVGo/Rplot311.png ...
written 6 months ago by jivarajivaraj0
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Comment: C: Single cells batch effects
... Sorry, I have bulk RNA-seq and single cell RNA-seq (iCELL8) on the same organism, in 9 time points. so how I can remove batch effect between to datasets because PCA analysis shows two strata of groups each correspond to bulk or single cell seq   ...
written 6 months ago by jivarajivaraj0
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Comment: C: gene dispersion, what does it mean?
...   Sorry, I have single cell seq data. I have 209 cells for a time point, I have two genes for which I want to know actually gene with higher expression in 209 cells in this time point Gene A mean=2.71 sd=1.05 biological coefficient of variation (BCV)= 0.37 Gene B mean=   2.27 sd= 0.922 biological ...
written 7 months ago by jivarajivaraj0
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Comment: C: DESeq2 time series analysis
...     Sorry I have a treatment and control over time points with two replication. I want to compare for example 2h in treatment vs 16h in control but whatever I try all comparisons are about 0 vs another time points   > coldata = data.frame(row.names=colnames(mergedd), Platform = as.factor(c(re ...
written 7 months ago by jivarajivaraj0

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