User: shuvadeep.maity

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Posts by shuvadeep.maity

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Comment: C: Heatmap vs heatmap.2
... Will try complexheatmap. Thanks ...
written 7 months ago by shuvadeep.maity0
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Comment: C: Heatmap vs heatmap.2
... 'but not running with the whole data sets" I mean to say it starts running and that stage everything looks like freeze, I need to force quit R to get out of this. ...
written 7 months ago by shuvadeep.maity0
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Comment: C: Heatmap vs heatmap.2
... 'but not running with the whole data sets" I mean to say it starts running and that stage everything looks like freeze, I need to force quit R to get out of this. ...
written 7 months ago by shuvadeep.maity0
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Heatmap vs heatmap.2
... I want to make a heat map without row and column clustering to keep my row order as it is. It has ~8000genes. (Row 8206 column 14) My commands are for heatmap: ``` y <- read.csv ('inputdata.csv', row.names = 'Gene_Name', header = TRUE) hmcol <- colorRampPalette(brewer.pal(10,"RdBu"))(256) ...
annotation written 7 months ago by shuvadeep.maity0 • updated 7 months ago by James W. MacDonald51k
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How to get the order of the gene list and indivdual cluster from the big heatmap made by heatmap2.0?
... I hav a data set with expression of around ~8000 genes with 2 replictes and two conditions Now I plotted the heatmap using heatmap2 with row clusterring (see below) > y <- read.csv('test.CSV', row.names = 'Gene_name', header = T) > head(y) R1_12 R2_12 ...
annotation heatmap written 8 months ago by shuvadeep.maity0 • updated 8 months ago by James W. MacDonald51k
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Comment: C: Limma time course experiments
... Thank you for the explanation ...
written 9 months ago by shuvadeep.maity0
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Limma time course experiments
... In limma manual, the example of time course experiment (Section 9.6) the target frame showed 2 replicates of 0hr wt and mutant but why it was not considered in the levels or in design? Can anyone please explain the discrepancy? The example, "we consider here a two-way experiment in which time cours ...
limma written 9 months ago by shuvadeep.maity0
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Comment: C: limma for getting DEGs from my own input matrix
... Thank you Aaron for your explanations/help. Much Appreciated! ...
written 9 months ago by shuvadeep.maity0
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Comment: C: limma for getting DEGs from my own input matrix
... Thank you Aaron for your explanations/help. Much Appreciated! ...
written 9 months ago by shuvadeep.maity0
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limma for getting DEGs from my own input matrix
... Hi I have normalized RNAseq data for treatment and control of a particular cell line. The matrix is the log expression ratio(12hrs_con/0hrs)and (12hrs_trated/0hrs). Can I use limma to get the DEGs using the my matrix as direct input file? #I have 2 replicates (each with control and treatment). I d ...
limma written 9 months ago by shuvadeep.maity0 • updated 9 months ago by Aaron Lun25k

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