User: krushnach80

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krushnach80300
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Posts by krushnach80

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Comment: C: Clustering of DAVID gene enrichment results from gene expression studies
... okay will give it a try thank for your quick response ...
written 5 days ago by krushnach80300
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Comment: C: Clustering of DAVID gene enrichment results from gene expression studies
... okay but when i go for the clustering of multiple sample of different lineages so i don;t do any statistical test just VST or rlog for wgcna ..so i get modules which im doing ontology so in this case i don;t have any file for statistical test unless i do it for all the samples.. ...
written 5 days ago by krushnach80300
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Comment: C: Clustering of DAVID gene enrichment results from gene expression studies
... okay only gene list so my input which is my final filtered list of gene which im giving input can be my sigGenelist ,that what i understand ...
written 5 days ago by krushnach80300
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Comment: C: Clustering of DAVID gene enrichment results from gene expression studies
... @Kevin you have a topMatrix object here , but i did clustering and taking some of the clustered gene set and giving that as input to david so what is my top matrix as im doing wgcna so there is no differential expression analysis involved so the only thing i have gene list from modules ..any sugge ...
written 5 days ago by krushnach80300
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Comment: C: TCGA miRNA Seq data analysis
... okay i will see the star manual..and if any issue i will write you back.. ...
written 4 weeks ago by krushnach80300
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Comment: C: TCGA miRNA Seq data analysis
... Im always elated when you respond yes im looking for bulk rna seq ,I do have normal sample but what i found long back that all of them are rsem normalised so what Im thinking is I do have normal sample i would use star aligner and make them rsem normalised to make comparison hope this would work... ...
written 4 weeks ago by krushnach80300
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Comment: C: New gencode gtf version for analysis
... "Generally, so long as you clearly state your version" yeah exactly this was my concern and yes for my own sake i do look into HUGO to map protein coding genes to filter things which are not needed ... "what are the extra genes?; are they important for your experiment? They may just be previously a ...
written 6 weeks ago by krushnach80300
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Comment: C: New gencode gtf version for analysis
... Im using GRCh38 as my build, as of now im mostly interested in protein coding genes ,but yes may be lon-non coding but i did a rough comparison between v21 and v28 i see the number genes in v28 is 58381 where as for v21 it's 60155 similarly the protein coding genes in v21 is 19881 and for v28 its 1 ...
written 6 weeks ago by krushnach80300
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New gencode gtf version for analysis
... I been using gencode 21 as my annotation file ,but the last update is gencode v28 , yes the new version comes with more accuracy and improvements would it going to make a drastic change into my results if i use the new version of annotation ? ...
rna-seq written 6 weeks ago by krushnach80300
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Comment: C: Java TreeView like tools
... @rleach I guess i can give it a try it won;t be an issue i suppose.. ...
written 7 weeks ago by krushnach80300

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