Question

How to figure out the FC value from Limma

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beslinail • 0

@d4a633b9

Last seen 9 months ago

Turkey

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Code should be placed in three backticks as shown below


I have an output file from the Limma package using GEO2R. I attached the file. you will see the FC column some value is as scientific notation (-1,97E+14) or some are integer number, some of them are meaningless such as `282.311.618.510.231` in Foldchange value. I need to help to figure out such value what it is. It depends on FC values to decide which gene is up or downregulated. I also converted to logFC colomn from character to numeric. some of them was changed the NA

Nail

ENSEMBL                           logFC                   adj.P.Val
ENSG00000160323 246.249.360.536.749 0.00189902833246103
ENSG00000114573 282.311.618.510.231 0.0132730794996708
ENSG00000126247 624.874.186.717.992 0.000234477864256105
ENSG00000163320 610.289.734.587.128 0.000181506020252273
ENSG00000144619 27.089.194.476.964  0.00429439674192473
ENSG00000187955 287.410.280.827.616 0.0353737404558676
ENSG00000104408 282.311.618.510.231 0.0132730794996708
ENSG00000110723 246.249.360.536.749 0.00189902833246103
ENSG00000196924 61.889.081.352.318  0.000109805220671758
ENSG00000116478 27.089.194.476.964  0.00429439674192473
ENSG00000105835 556.805.058.106.797 0.00272800655111703
ENSG00000090273 282.311.618.510.231 0.0132730794996708
ENSG00000167693 27.089.194.476.964  0.00429439674192473
ENSG00000173599 287.410.280.827.616 0.0353737404558676
ENSG00000067992 565.429.938.384.731 0.00189902833246103
ENSG00000090857 246.249.360.536.749 0.00189902833246103
ENSG00000141959 246.249.360.536.749 0.00189902833246103
ENSG00000132554 246.249.360.536.749 0.00189902833246103
ENSG00000132669 246.249.360.536.749 0.00189902833246103
ENSG00000179134 246.249.360.536.749 0.00189902833246103
ENSG00000093183 246.249.360.536.749 0.00189902833246103
ENSG00000131171 27.089.194.476.964  0.00429439674192473
ENSG00000125676 246.249.360.536.749 0.00189902833246103
ENSG00000118900 812.822.411.115.588 1,35E-03
ENSG00000199085 0.781732032845079   0.00429439674192473
ENSG00000208023 -1,97E+14   0.005974890214727
ENSG00000210741 2,46E+14    0.00189902833246103
ENSG00000284485 5,48E+14    0.0142686384742479
ENSG00000265820 -4,77E+14   0.0364657232194689
ENSG00000199168 -4,91E+14   0.00189902833246103
ENSG00000199107 -2,96E+14   1,60E+09


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

limma DEGseq DifferentialExpression • 906 views

ADD COMMENT • link updated 23 months ago by Kevin Blighe ★ 3.9k • written 23 months ago by beslinail • 0

1

Entering edit mode

That’s an Excel problem, not a GEO/R problem or related to limma and Bioconductor.

ADD REPLY • link 23 months ago ATpoint ★ 4.0k

0

Entering edit mode

Thanks alot for the feedback. I also read the file.tsv in R but

logFC
246.249.360.536.749
282.311.618.510.231
624.874.186.717.992
610.289.734.587.128
27.089.194.476.964
287.410.280.827.616
282.311.618.510.231
246.249.360.536.749
61.889.081.352.318
27.089.194.476.964
556.805.058.106.797
282.311.618.510.231
27.089.194.476.964
287.410.280.827.616
565.429.938.384.731
246.249.360.536.749
246.249.360.536.749
246.249.360.536.749
246.249.360.536.749
246.249.360.536.749
246.249.360.536.749
27.089.194.476.964
246.249.360.536.749
287.410.280.827.616
246.249.360.536.749
246.249.360.536.749
27.089.194.476.964
570.956.330.869.753
246.249.360.536.749
510.586.159.454.785
246.249.360.536.749
556.610.827.099.487
282.311.618.510.231
-483.811.467.917.233
246.249.360.536.749
-467.267.181.390.415
535.999.796.111.941
0.781732032845079
-197.267.617.193.309
246.249.360.536.749
548.454.313.754.696
-477.154.337.629.934
-490.538.838.231.324
-227.677.095.984.221
27.089.194.476.964
-241.242.779.010.798
-385.991.866.384.134
-450.083.589.186.891
-457.928.054.310.547
639.502.161.812.812
-533.290.416.109.379
-378.009.601.004.809
246.249.360.536.749
-487.652.856.027.402
0.996147266786311
510.411.554.969.318
494.580.540.986.119
222.777.139.955.666
524.929.906.894.337
27.089.194.476.964
-503.633.161.518.072
484.775.916.020.841
540.887.837.835.975
-573.375.417.698.973
589.404.603.625.191
-485.547.100.658.291
472.362.686.301.098
444.778.071.539.014
631.605.121.378.522
246.249.360.536.749
246.249.360.536.749
588.195.120.310.517
602.729.380.838.246
246.249.360.536.749
-46.411.469.941.686
282.311.618.510.231
346.350.794.393.807
542.359.179.541.148
246.249.360.536.749
607.262.217.977.164
27.089.194.476.964
550.373.772.802.455

ADD REPLY • link updated 23 months ago by Kevin Blighe ★ 3.9k • written 23 months ago by beslinail • 0

0

Entering edit mode

You probably have opened that file in Excel before. Get it again directly from GEO2R, or even better take the R script GEO2R offers and run it in R manually. When you want to write things as Excel later to distribute I usually use the openxlsl package which does a good job setting cell categories in a way that this nonsense gibberish does not happen, nor gene2date conversion happens.

ADD REPLY • link 23 months ago ATpoint ★ 4.0k

0

Entering edit mode

I tried to FC column to dbl from chr. But FC colomn is changed by NA

genlist_filter <- read_csv(file = "AD_control5.csv")

genlist_filter
sapply(genlist_filter, class)

cols.num <- c("logFC")
genlist_filter[cols.num] <- sapply(genlist_filter[cols.num],as.numeric)
sapply(filtered_genes, class)

ADD REPLY • link updated 23 months ago by Kevin Blighe ★ 3.9k • written 23 months ago by beslinail • 0