User: amy16

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amy160
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Posts by amy16

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Comment: C: Error and warning message when reading the ballgown object
... I checked the i_data.ctab files and found that the ids are different. So, is there anything I can do to fix it? -Amy ...
written 5 months ago by amy160
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Error and warning message when reading the ballgown object
... Hi, I am using Ballgown as apart of the tuxedo suite for DEG, and I get this warning message while reading the ballgown object, > pheno_data01<-read.csv("/fast/a123456/Analysis02/DGE/prr01/prr01.csv") > bg<-ballgown(dataDir="/fast/123456/Analysis02/DGE/prr01", pData=pheno_data01, samp ...
illumina software error deg ballgown tuxedo written 5 months ago by amy160 • updated 5 months ago by James W. MacDonald47k
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Ballgown data read error
... Hi, When reading the ballwgown object I get the following error message: Error in ballgown(dataDir = "/fast/users/a123456/Analysis02/DGE/prr01",  :   intron ids were either not the same or not in the same order across samples. double check i_data.ctab for each sample. Please advise me in fixing th ...
software error ballgown written 5 months ago by amy160
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Subset functionin R
... Hi all, When you make subset before performing the stattest for gene as the feature, do you change the, texpr in the below script to gexpr or does texpr subset can also be used to calculate the stattest for gene feature too? Script : bg_chrX_filt <- subset(bg_chrX, "rowVars(texpr(bg_chrX)) &g ...
rnaseq R ballgown written 7 months ago by amy160
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Accessing the assembly data-output
... Hi all, I am accessing the assembly data to calculate the fold change. The command I had used: > transcript_fpkm=texpr(bg_filt, 'FPKM') > write.csv(transcript_fpkm, file="B1transcript.csv") > head(transcript_fpkm) FPKM.B1C_01 FPKM.B1T_01 5 3.073159 1.206581 18 0.000000 ...
rnaseq R ballgown written 7 months ago by amy160
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Comment: C: Error in stattest function
... Once the fold change for each of the transcript/ gene/ exon has been done between the two samples, is it possible to integrate within the ballgown function to determine the differential expression? ...
written 7 months ago by amy160
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Comment: C: Error in stattest function
... Thanks Alyssa for the reply and the good news that I can rank the genes/transcripts by fold change. Is this fold change calculation script described in the Ballgown manual? Can u please direct me on how I go about it? PS: I understand and I totally agree with you that without replicates, one can no ...
written 7 months ago by amy160
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Error in stattest function
... Hi all, Please let me know how I should go about in fixing this error. > pData(bg) ids treatment genotype 1 B1C_01 control resistant 2 B1T_01 inoculated resistant > prr01_trans_result=stattest(bg_filt, feature="transcript", covariate="treatment", getFC=TRUE, meas="FPKM") Error in ...
rnaseq R ballgown written 7 months ago by amy160 • updated 7 months ago by Alyssa Frazee200
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Comment: C: Error in reading ballgown object
... Hi Alyssa, Thanks for the suggestion. It was helpful. and I was able to get over that error. ...
written 7 months ago by amy160
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Error in reading ballgown object
... Hi, Can someone please advise me on this error? > pheno_data   ids  treatment    genotype 1 B1C    control   Resistant 2 B2C    control Susceptible 3 B3C    control   Resistant 4 B4C    control Susceptible 5 B1T inoculated   Resistant 6 B2T inoculated Susceptible 7 B3T inoculated   Resistant 8 B ...
R ballgown written 8 months ago by amy160 • updated 8 months ago by Alyssa Frazee200

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