User: elhamdallalbashi

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Posts by elhamdallalbashi

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Comment: C: log2 fold change in result of DEseq2
... Hello Michael, if you remember, I wanted to do DE for all treated vs all controls samples.and you suggested me a design of ~experiment + condition, I need DE for co-expression network,so for coding and non coding I did that,but I see that there are a variety value in log2 fold change.I can not unde ...
written 2.6 years ago by elhamdallalbashi0
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log2 fold change in result of DEseq2
... Hello, I have a question about influence of log2 fold change in determining best genes in differential expression of DEseq2,as an example with adjusted p-value < 0.1,I have 23 genes, out of 26998 with nonzero total read count adjusted p-value < 0.1 LFC > 0 (up) : 10, 0.037% LFC < 0 ...
deseq2 written 2.6 years ago by elhamdallalbashi0 • updated 2.6 years ago by Michael Love25k
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Comment: C: the statistical test that DESeq2 use
... Thanks for the quick and helpful response ...
written 2.6 years ago by elhamdallalbashi0
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the statistical test that DESeq2 use
... Hello All, for estimating the differential expression values,what statistical test does DEseq2 use for estimating the differential expression values,is it t-test, Fisher exact test or some other? ...
deseq2 statistics written 2.6 years ago by elhamdallalbashi0 • updated 2.6 years ago by Ryan C. Thompson7.4k
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Comment: C: DEseq2 for several experiments with one condition
... and I have a question about design,as you know I have 2 column in coldata,that one of them is the rownames of coldata that it should be like the columns of countdata,how can I have two header in coldata (experiment + condition)?I received an error. only in this situation I do not receive an error,i ...
written 2.7 years ago by elhamdallalbashi0
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Comment: C: DEseq2 for several experiments with one condition
... I should say that,each experiment is effect of one drug on one cancer (drugs and cancers are different in each experiment ) but the platform is similar and all of them are Illumina HiSeq 2000 (Homo sapiens). Regardless of the type of drug and cancer I want DE of all treatment vs. all control. ...
written 2.7 years ago by elhamdallalbashi0
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Comment: C: DEseq2 for several experiments with one condition
... Hi Michael, this is my colData A1 control A2 control A3 control A4 treatment A5 treatment A6 treatment B1 control B2 control B3 control B4 treatment B5 treatment ...
written 2.7 years ago by elhamdallalbashi0
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Comment: C: DEseq2 for several experiments with one condition
... in previous question I want to know DEseq2 is right choice or not,in this post I need help for a workflow because I could not understand pathway of DEseq2  ...
written 2.7 years ago by elhamdallalbashi0
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Comment: C: DE by DEseq2
... I have 9 experiments that each experiment is effect of one drug on one cancer (drugs and cancers are different in each experiment ) but the platform is similar and all of them are Illumina HiSeq 2000 (Homo sapiens). My data from RNA-seq analysis are not normalize. ...
written 2.7 years ago by elhamdallalbashi0
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Comment: C: DE by DEseq2
... thank you for a reply.you mean for importing data I should provide a matrix with all of treatment and control samples of all experiments? ...
written 2.7 years ago by elhamdallalbashi0

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