User: kritikamish99

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India
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Posts by kritikamish99

<prev • 45 results • page 2 of 5 • next >
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How to filter all column using Loop
... I have 100 columns 1 column is name and 2 to 100 samples values I want to filter out column 2 to 100 with certain threshold say >=5 using loop. This will iterate for new file name corresponding to sample name. for example filtering value above 5 Col1 Col2 Col3 Col4 Col5 Col6 Col7 A 5 1 1 2 4 1 ...
filter loop written 23 months ago by kritikamish9910 • updated 23 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Tac and Bioconductor giving different results
... Hi Steve I was able to reproduce same results from both the methods Actually the out put file which i got from bioconductor was logged and TAC gives FC as unlogged after converting to antilog to my data i was able to get same results   ...
written 23 months ago by kritikamish9910
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Comment: C: Tac and Bioconductor giving different results
... Hi Steve I was performing u133a2 affymetrix gene expression study The normalisation method which i used was MAS5 After that i did FC calculation manually and then logFC manually too over exprs data that is eset i am getting different results compare to TACs . For example in column i am getting F ...
written 23 months ago by kritikamish9910
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Tac and Bioconductor giving different results
... Hi The questions may seem very general please bear! I have done analysis using TAC affymetrix software and bioconductor affy package the result are not showing similarity between both Which method i should go for TAC or Bioconductor ...
bioconductor results tac reproducbiltiy written 23 months ago by kritikamish9910 • updated 23 months ago by Steve Lianoglou12k
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Comment: C: mas5 normalisation giving negetive value after using exprs()
... Hi Gordon Exactly!!! This is for older affymetrix chip and they have different version of MAS5(prior was MAS4). But my exprs() is giving me negative value. not sure whether MAS5 is logged or MAS4 or earlier is unlogged!!!     ...
written 23 months ago by kritikamish9910
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Comment: C: mas5 normalisation giving negetive value after using exprs()
... Hi Gordon Can you give me any source that say MAS5 output is log-scale value As per my knowlegde MAS algorithm outputs the unlogged scale value ...
written 23 months ago by kritikamish9910
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mas5 normalisation giving negetive value after using exprs()
... Hi all I used Mas5 normalisation over my cel file. After normalisation i have done exprs() call I am getting negetive value for this I have not any fold change or log FC over this data   Code :- setwd("MCF7/data") cels = list.files("MCF7/data", pattern = ".CEL") raw.data=ReadAffy(verbose=TRUE, ...
normalization mas5 exprs written 23 months ago by kritikamish9910 • updated 23 months ago by James W. MacDonald51k
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How to take mean from specific column
... Hi I have column of gene expression  of 208 (104X2) samples. I want to take mean of all replicates using R loop Can any one suggest me   w x y a b e 5 1 1 2 4 1 6 2 2 5 3 6 7 3 3 8 9 3 8 4 6 9 1 3 so for example i have have w x y a b e columns i want to take avaerage of w and x, y and a , b and e an ...
R mean written 23 months ago by kritikamish9910 • updated 23 months ago by Gordon Smyth38k
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Comment: C: Error in ball gown command
... Okay but I want to find differential expression analysis on W1 vs M1 and W2 vs M2. I can't perform ball gown diff estimation with this? For bal gown minimum how many sample one need?? ...
written 2.9 years ago by kritikamish9910
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Error in ball gown command
... Hello All I have 4 samples M1 , M2 , W1, W2 . I have done alignment with Ecoli ref genome usng hisat2 on this sample i ran stringtie for abundance estimation  Now i am trying to run ball gown on this samples of now i tried this commands: data_directory <- "/Hisat_stringtie_/string_out/" bg = ba ...
rnaseq differential gene expression ballgown written 2.9 years ago by kritikamish9910 • updated 2.9 years ago by Jeff Leek560

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Popular Question 14 months ago, created a question with more than 1,000 views. For Illumina ID Mapping library
Popular Question 2.9 years ago, created a question with more than 1,000 views. For how to use idat file for analyses in bioconductor

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