User: dickson.russel

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Posts by dickson.russel

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Comment: C: 2 cells X 2 conditions X patients
... Thank you for your reply, Michael.  Regarding X/Y or Y/X both fold-change values are not matching with the relative expression values. Could it be because of higher FDR values? I do agree with your comment on FDR cut-off.    ...
written 8 months ago by dickson.russel10
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Comment: C: 2 cells X 2 conditions X patients
... Hi Michael: After getting DEGs using contrast = list("cndT.cellY", "cndC.cellY"), I have notified some unusual observations : 1. the fold change (or logfc) doesn't match with the expression pattern of several genes for two different groups. For example,  say gene-x has down patterns in group X but ...
written 8 months ago by dickson.russel10
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Comment: C: 2 cells X 2 conditions X patients
... Michael - thank you very much for your diligent feedback and detailed explanation which is very much appreciated. Regarding relevel(), you correctly guessed that I copied/pasted before adding relevel(), therefore, the interested names are as you mentioned i.e. cndC.cellY and cndT.cellY. Again, tha ...
written 8 months ago by dickson.russel10
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Comment: C: 2 cells X 2 conditions X patients
... Michael - thank you for your reply. I want the exact interaction what you have mentioned in your response i.e.  Y vs X effect for C and for T, or to contrast that effect between T and C, specially contrast between T(Y/X) and C(Y/X). Can you please check my the below approach, if I am doing correct ...
written 8 months ago by dickson.russel10
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Comment: C: 2 cells X 2 conditions X patients
... Hi Michael: Thank you for your suggestion and the link. I have applied the model as suggested in vignettes by creating an additional column i.e. (ind.n) ds <- DESeqDataSetFromMatrix(countData=counts, colData=samples, design=~cell+cell:ind.n+cell:cnd) here cnd=condition ds$cell <- relevel(ds ...
written 8 months ago by dickson.russel10
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2 cells X 2 conditions X patients
... Hi, I've a small question concerning differential expression analysis regarding 12 samples divided into 2 cell lines (cell 1 & 2), two conditions: tumor (T) and control (C): Cell Condition Patient number (p) Cell1 T 1 Cell1 T 2 Cell1 T ...
deseq2 written 8 months ago by dickson.russel10 • updated 8 months ago by Michael Love18k
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Comment: C: 2 cells x 2 media x 2 conditions
... Gavin - Thank you for taking the time to explain in details. I appreciate your time and help. ...
written 9 months ago by dickson.russel10
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Comment: C: 2 cells x 2 media x 2 conditions
... Gavin - thank you for your reply. Q2: Sorry for being not very clear about my question2. I want to obtain those genes which are responding more (more up- or more down-regulated in [medium2(treated/control) vs medium1(treated/control) of cellline2] VS. [medium2(treated/control) vs medium1(treated/co ...
written 9 months ago by dickson.russel10
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2 cells x 2 media x 2 conditions
... I have a RNA-seq experiment with the following design:  EDF cell line media treatment cellline1 medium1 ctrl cellline1 medium1 ctrl cellline1 medium1 ctrl cellline1 medium1 treated cellline1 medium1 treat ...
deseq2 written 9 months ago by dickson.russel10 • updated 9 months ago by Gavin Kelly550

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